Bgee: Gene Expression Evolution

Expression data retrieved for the gene ENSMUSG00000091474: 2610021A01Rik - at the stage: "infant" - Mus musculus

Query parameters
Stage: infant
Gene: ENSMUSG00000091474 - 2610021A01Rik
Data parameters
[?] [?]

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Affymetrix experiment E-MEXP-1623

Experiment name Transcription profiling of skeletal muscle from wild type and mdx mice at three time points [E-MEXP-1623]
Source ArrayExpress
Experiment description In this study, in order to minimize the genetic variability of muscle samples we have used two approaches. First, we have analyzed the gene expression profile from a single skeletal muscle, the medial gastrocnemius (MG), and not from a pool of different muscles which could have different expression profiles. Second, we have performed the temporal gene expression profiling by extracting the MG muscles of the same individual from the both legs at two different times to minimize the inter-individual genetic variability. The MG muscle represent an excellent candidate for biopsy due to its easy accessible by surgery and also because its biopsy is well tolerated by the animals allowing us to perform another later biopsy in the other leg to obtain two MG samples of the same individual at two different times. Moreover, MG muscle is composed of approximately 20-30% type I (red) fibers and 70-80% type II (white) fibers {Ariano MA, 1973}, {Simard C, 1988}, {Zhan WZ, 1992} and therefore is more representative of skeletal muscle tissue in general than a muscle composed exclusively by red or white fibers.<br><br><br><br>The transcript expression profiles in MG muscles from mdx and wild-type mice were analyzed at 3 weeks, 1.5 months and 3 months of life by using the 430 2.0 gene chips from Affymetrix (n=3 for each condition). The differentially expressed transcripts which showed differences ?1.5-fold were obtained by performing three different comparisons: 1) genes differentially expressed in mdx compared with controls at each point in time (additional file 1); 2) temporal analysis of the genes differentially expressed in mdx mice between the three points in time also compared with the variations in control mice (additional file 2); and 3) temporal analysis of the genes differentially expressed in control mice between the three points in time also compared with the variations in mdx mice (additional file 3). The first comparison that we performed, by comparing the gene expression between mdx and control mice at every point in time, was similar to that performed in previous longitudinal studies {Porter JD, 2003}, {Rouger K, 2002}, {Turk R, 2005}. However, the other two comparisons were directed to elucidate the genes that are varying throughout the period of time analyzed in every mice strain, and therefore we obtained on the one hand the genes that vary in mdx mice but not in wild-type, and on the other hand the genes that vary in control animals but remain unchanged in mdx mice between the times analyzed. To present the results in a more comprehensive form, all the genes were classified in seven different categories: Cell adhesion & extracellular matrix; Proteolysis; Muscle structure & regeneration; Inflammation & immune response; Cell signaling & cell communication; Metabolism; and Others/unknown. The resulting genes from our study were classified in their functional categories using information from Affymetrix (www.affymetrix.com) and from the Gene Ontology database accessible in the Jackson Laboratory Mouse Genome Informatics website (www.informatics.jax.org).<br><br>
Chips
  • Chip ID: C2 - Annotation by Bgee curators: Anatomical structure ID: MA:0002306 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: C1 - Annotation by Bgee curators: Anatomical structure ID: MA:0002306 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: C3 - Annotation by Bgee curators: Anatomical structure ID: MA:0002306 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment E-MEXP-1853

Experiment name Transcription profiling of mouse fetal and early adult liver [E-MEXP-1853]
Source ArrayExpress
Experiment description trascriptional profiling of mouse fetal liver during development
Chips
  • Chip ID: MG_U74Bv2_W2 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 115374_r_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
  • Chip ID: MG_U74Bv2_W1 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 115374_r_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
  • Chip ID: MG_U74Bv2_W3 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 115374_r_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality

Affymetrix experiment E-MEXP-242

Experiment name Transcription profiling of wild type and Clcn7-/- mouse hippocampus at p14 [E-MEXP-242]
Source ArrayExpress
Experiment description Comparison of expression levels between wild type and Clcn7-/- mouse hippocampus at p14. 3 wild type and 3 mutant mice were studied.
Chips
  • Chip ID: C7_335wt_B2 - Annotation by Bgee curators: Anatomical structure ID: MA:0000191 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 115374_r_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
  • Chip ID: C7_240wt_B - Annotation by Bgee curators: Anatomical structure ID: MA:0000191 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 115374_r_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: C7_338wt_B - Annotation by Bgee curators: Anatomical structure ID: MA:0000191 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 115374_r_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality

Affymetrix experiment E-MEXP-634

Experiment name Transcription profiling of Gata3 conditional knock out mice to investigate epidermis and hair follicle differentiation [E-MEXP-634]
Source ArrayExpress
Experiment description Transcriptome analysis on Gata3 conditional knock out murine hair follicles. Background. The transcription factor Gata3 is critically involved in epidermis and hair follicle differentiation. Yet, little is known about how Gata3 co-ordinates stem cell lineage determination in skin, which processes are mostly implicated and how Gata3 differentially regulates distinct cell populations within the hair follicle. Here, we describe a conditional Gata3-/- mouse (K14-Gata3-/-) in which Gata3 is specifically deleted in epidermis and hair follicles. Principal findings. K14-Gata3-/- mice show aberrant postnatal growth and development, delayed hair growth and maintenance, abnormal hair follicle organization and irregular pigmentation. After the first hair cycle, the germinative layer surrounding the dermal papilla was not restored; instead, proliferation was pronounced in basal epidermal cells. Transcriptome analysis of laser-dissected K14-Gata3-/- hair follicles as compared to wild type littermate controls, revealed mitosis, epithelial differentiation and the Notch, WNT and BMP signalling pathways to comprise significantly overrepresented processes. Conclusions. Subsequent elucidation of these pathways at the RNA and protein levels and physiologic endpoints shows that Gata3 integrates diverse signalling networks to regulate the balance between hair follicle and epidermal cell fates.
Chips
  • Chip ID: 10wt - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: 7wt - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: 3wt - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: 8wt - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: 1wt - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: 5wt - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment E-MEXP-733

Experiment name Transcription profiling of skeletal muscle from wild type and Nebulin knock-out mice [E-MEXP-733]
Source ArrayExpress
Experiment description Knock out of the Nebulin gene. We compared the Quadriceps of two Nebulin -deficient vs. 2 Wildtype mice. The two KO-WT pairs derived from two litters (F2 generation, background: C57/Bl6 and 129/IB10).
Chips
  • Chip ID: Witt_300605_N87_MOE430_2 - Annotation by Bgee curators: Anatomical structure ID: MA:0002363 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: Witt_180705_N06_MOE430_2 - Annotation by Bgee curators: Anatomical structure ID: MA:0002363 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment E-MEXP-834

Experiment name Transcription profiling of liver from Ercc1-/- mice and wild type littermates to investigate features of premature aging [E-MEXP-834]
Source ArrayExpress
Experiment description To investigate the cause of the premature aging features in the Ercc1-/- mouse, we compared the entire transcriptome of the Ercc1-/- mouse liver to that of wildtype littermates at the age of 15 days, when the Ercc1-/- mice reached their maximal weight and had symptoms of progeria, yet overall pathology was still limited. The liver was selected because the tissue showed several well-defined histological changes associated with aging (polyploidy and intranuclear inclusions) as well as evidence that it is responding to endogenous genotoxic stress (stabilized p53).
Chips
  • Chip ID: WT11 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WT10 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WT7 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WT9 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WT12 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WT8 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment E-MEXP-835

Experiment name Transcription profiling of liver from Csbm/m/Xpa-/- knockout mice to investigate the effect of nucleotide excision repair pathway inactivation [E-MEXP-835]
Source ArrayExpress
Experiment description Cockayne syndrome (CS) is a photosensitive, DNA repair disorder associated with progeria caused by a defect in the transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER). Here, complete inactivation of NER in Csbm/m/Xpa-/- mutants causes a phenotype that reliably mimics the human progeroid CS syndrome. Newborn Csbm/m/Xpa-/- mice display attenuated growth, progressive neurological dysfunction, retinal degeneration, cachexia, kyphosis and die before weaning. To investigate whether a disturbance in growth and metabolism could explain the pronounced accelerated organismal deterioration seen in Csbm/m/Xpa-/- mice, we evaluated the liver transcriptome of 15-day old wt, single and double mutant mice (n=4). At this age, the Csbm/m/Xpa-/- pups have not yet become cachectic. Mouse liver transcriptome analysis and several physiological endpoints revealed systemic suppression of the GH/IGF1 somatotroph axis and oxidative metabolism, increased antioxidant responses, hypoglycemia together with hepatic glycogen and fat accumulation. Broad genome-wide parallels between Csbm/m/Xpa-/- and naturally aged mouse liver transcriptomes suggested that these changes are intrinsic to natural aging and the DNA repair-deficient mice. Importantly, wild type (wt) mice exposed to a low dose of chronic genotoxic stress and adult Csbm/m mutant mice recapitulated this response, thereby pointing to a novel link between genome instability and the age-related decline of the somatotroph axis.
Chips
  • Chip ID: csb-xpa4 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: csb-xpa1 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: csb-xpa2 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: csb-xpa3 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment E-MEXP-840

Experiment name Transcription profiling of aorta from mice underexpressing Fibulin-4 to investigate its role in elastic fibre assembly and cardio-vasuclar disease [E-MEXP-840]
Source ArrayExpress
Experiment description Extracellular elastic fibres apply structure and mechanical elasticity to organs such as large arteries, lungs and skin 1. Elastic fibres are assembled through polymerization of tropoelastin monomers and loss of elastin is associated with aneurysmal degeneration of the aorta 2. The Fibulins are a six-member protein family hypothesized to function as intermolecular bridges that stabilize the organization of extracellular matrix structures such as elastic fibres and basement membranes 3. Fibulin-4 is found in the medial layers of arteries and moderately expressed in heart valves 4. To examine a potential role of Fibulin-4 in elastic fibre assembly and cardio-vascular disease we generated a mouse model underexpressing Fibulin-4. To get insight into the underlying molecular pathways involved in aneurysm formation, we determined the aorta transcriptome of Fibulin-4R/R animals and identified biological processes that were significantly overrepresented including apoptosis and cell death as well as several novel gene targets implicated in the response to aortic failure. We conclude that decreased Fibulin-4 expression causes aberrant composition of the elastin layers in the aorta and valvular leaflets, resulting in aortic aneurysms and heart abnormalities.
Chips
  • Chip ID: WM2 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WM4 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WM3 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: WM1 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE10347

Experiment name Transcription profiling of mouse Hexose-6-phosphate dehydrogenase knockout muscle at 4 weeks [GSE10347]
Source GEO
Experiment description Hexose-6-phosphate dehydrogenase (H6PD)is the initial component of a pentose phosphate pathway inside the endoplasmic reticulum (ER) that generates NADPH for ER enzymes. In liver, H6PD is required for the 11-oxoreductase activity of 11ss-hydroxysteroid dehydrogenase type 1 (11ss-HSD1), which converts inactive 11-oxo glucocorticoids to their active 11-hydroxyl counterparts; consequently, H6PD null mice are relatively insensitive to glucocorticoids, exhibiting fasting hypoglycemia, increased insulin sensitivity despite elevated circulating levels of corticosterone, and increased basal and insulin-stimulated glucose uptake in muscles normally enriched in Type II (fast) fibers which have increased glycogen content. They also display a progressive vacuolar myopathy evident after 4 weeks of age. We carried out microarray analysis on TA and soleus muscles from 4 week old WT and KO mice to determine an expression profile predicting myopathy. Experiment Overall Design: 4 week old mice are weaned and do not display overt histological evidence of myopathy. Soleus and tibialis anterior are used as comparison groups as they have distinct fibre type content and differing metabolic properties. 3 biological replicates are used for each genotpye and sample type.
Chips
  • Chip ID: GSM261512 - Annotation by Bgee curators: Anatomical structure ID: MA:0002424 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM261517 - Annotation by Bgee curators: Anatomical structure ID: MA:0002395 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM261516 - Annotation by Bgee curators: Anatomical structure ID: MA:0002395 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM261518 - Annotation by Bgee curators: Anatomical structure ID: MA:0002395 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM261510 - Annotation by Bgee curators: Anatomical structure ID: MA:0002424 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM261511 - Annotation by Bgee curators: Anatomical structure ID: MA:0002424 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE10587

Experiment name Transcription profiling of mouse stria vascularis from animals lacking Slc26a4 and heterzygous controls before the onset of hearing. [GSE10587]
Source GEO
Experiment description Determination of differential expression of genes in the stria vascularis of pendrin (Slc26a4) heterozygous and knockout mice before the onset of hearing at postnatal day 10 (P10). Experiment Overall Design: A total of Six samples of stria vascularis RNA obtained from P10 mice were analyzed. Triplicates from pendrin (Slc26a4) heterozygous and knockout mice were run and analyzed.
Chips
  • Chip ID: GSM266961 - Annotation by Bgee curators: Anatomical structure ID: MA:0000236 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM266953 - Annotation by Bgee curators: Anatomical structure ID: MA:0000236 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM266955 - Annotation by Bgee curators: Anatomical structure ID: MA:0000236 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE10889

Experiment name Transcription profiling of mouse lung from E18, P1, P4, P7, P10, P14, P21, and adult) or pooled (E12, E14, E16) - developmental series [GSE10889]
Source GEO
Experiment description Mammalian lung development is a complex morphogenetic process, which initiates near mid-gestation and continues through early postnatal life. The lung arises as two lateral buds that emerge from the ventral foregut endoderm at ~ 9 days after fertilization (in mouse) and undergo numerous rounds of dichotomous branching to form the bronchial tree. This stage of development is referred to as the pseudoglandular phase, histologically characterized by loose mesenchyme surrounding undifferentiated epithelial tubes. We have undertaken a comprehensive gene expression profiling of the entire process of murine lung development using oligonucleotide-based microarrays. Our data reveals the expression pattern of ~ 11,000 genes throughout the morphologic stages of lung development. Examination of the data confirms previously known patterns of expression for extracellular matrix genes and provides new information regarding relationships in temporal expression among groups of these genes. Large-scale cluster analysis reveals associations in the expression profile of specific genes with defined developmental processes. Experiment Overall Design: RNA was isolated from individual (E18, P1, P4, P7, P10, P14, P21, and adult) or pooled (E12, E14, E16) whole lungs using a modified guanidinium:phenol extraction method.Ten micrograms of total RNA was used to generate target cRNA for hybridization to Affymetrix Mu11K chipset subA and subB oligonucleotide microarrays. A single chip set was used for each time-point. Before target generation, individual RNA samples were pooled so that each target was derived from a minimum of three individual lungs.
Chips

Affymetrix experiment GSE11186

Experiment name Transcription profiling of mouse dorsal skin during hair follicle cycling [GSE11186]
Source GEO
Experiment description Hair follicles undergo continuous cycling of growth (anagen), regression (catagen), and relative quiescence (telogen) with a defined periodicity. Evolutionarily conserved hair follicle cycling is thought to provide mechanisms for controlling the length of hair in specific body sites, and to allow the periodic shedding of fur in response to seasonal changes in mammals. The periodicity of the hair growth cycle ranges from approximately three-weeks in synchronized hair follicles of mouse dorsal skin to several years in hair follicles of human scalp where the follicles undergo an extended period of anagen. Although numerous molecular pathways, including BMP signaling, have been implicated in the control of hair follicle cycling, the underlying mechanisms regulating its timing remain elusive. Taking a genomics approach to study gene expression during synchronized mouse hair follicle cycling, we discovered that CLOCK-regulated genes are regulated during the hair growth cycle, including prominent expression in the secondary hair germ during telogen and early anagen. Analysis of Clock and Bmal1 mutant mice revealed a delay in anagen progression, and the secondary hair germ cells show decreased levels of phosphorylated Rb and lack mitotic cells, suggesting the circadian clock regulates hair follicle cycling via its effect on the cell cycle. While circadian clock mechanisms have been implicated in a variety of diurnal biological processes, our data link circadian clock genes to biological oscillation that is weeks in duration. Experiment Overall Design: To investigate the molecular control of hair follicle cycling, we profiled mRNA expression in mouse dorsal skin at multiple representative time points in the synchronized second postnatal hair growth cycle and in a depilation-induced hair growth cycle. For profiling of second synchronized and depilation-induced hair growth cycle, the same upper-mid region of dorsal skin was excised from C57BL/6 mice at representative postnatal days (P). The time points for second hair growth cycle are classified into different phases of the hair growth cycle based on established morphological guidelines as follow: early anagen (P23, P25), mid anagen (P27), late anagen (P29, P34), early catagen (P37, P39), mid catagen (P41), and telogen (P44). Depilation-induced hair growth cycle by applying wax/rosin mixture on the dorsal skin of seven-week old mice (all follicles in telogen) was performed on mice. The corresponding phases of the hair growth cycle at number of days following depilation (D) is as follow: early anagen (D3), mid anagen (D5), late anagen (D8, D12), and early catagen (D17). For each time point, multiple biological replicates were profiled, with each mouse dorsal skin separately hybridized to an Affymetrix array.
Chips
  • Chip ID: GSM281782 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281780 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281779 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281781 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281785 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281786 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281788 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281783 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM281787 - Annotation by Bgee curators: Anatomical structure ID: MA:0000510 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE11764

Experiment name Transcription of mouse postnatal day (P) 14, 28, 60 visual cortex (V1) [GSE11764]
Source GEO
Experiment description Analysis of gene expression before (P14), during (P28), and after (P60) the critical period for ocular dominance plasticity. Experiment Overall Design: V1 from litters of mice were microdissected and processed for RNA extraction.
Chips

Affymetrix experiment GSE11899

Experiment name Transcription profiling of mouse Dicer-deficient liver [GSE11899]
Source GEO
Experiment description Background & Aims: MiRNAs are small (~22 nucleotide), non-coding RNA molecules that regulate gene expression through imperfect complementarity with target messenger RNAs. The function of miRNA in mammalian organogenesis is largely unknown. Conditional loss-of-function of Dicer, the enzyme that processes precursor miRNA transcripts into their mature, active form, has been shown to cause severe defects in a number of organ systems. Here we address the role of Dicer in liver development and function. Methods: Mice lacking Dicer function in hepatocytes were generated using an Afp-Cre strain to drive deletion of a floxed Dicer allele. Deletion of the flox-dicer allele was confirmed by quantitative PCR. Decreased miRNA levels detected by quantitative RT-PCR and in situ hybridization confirmed loss of Dicer function. Gene expression microarray analysis was performed on liver RNA from P28 mutant and control mice. Liver sections from mutant and control mice ranging from embryonic stages through 3-4 months of age were examined and liver function tests were performed on adult mice. Results: Mice lacking hepatocyte Dicer function were born alive at the expected frequency, and had grossly normal appearance and behavior. Despite the loss of mature miRNA, hepatic function was normal, as reflected by normal blood gludose, albumin, cholesterol, and bilirubin. However, mutant mice between 2-4 months of age exhibit progressive hepatocyte damage, elevated ALT/AST, with evidence of balanced proliferation and apoptosis in the lobule. Microarray analysis indicates large-scale changes in gene expression, with increased expression of many miRNA targets, as well as imprinted genes. Conclusions: Loss of miRNA processing in the liver at late gestation has a remarkably mild phenotype, suggesting that miRNAs do not play an essential role in hepatic physiology. However, miRNA deficiency results in hepatocyte apoptosis and balanced hepatocyte regeneration. Finally, microarray analysis of gene expression in mutant liver suggests a previously unrecognized role for Dicer in the repression of imprinted genes. Experiment Overall Design: Hepatic RNA was isolated from 5 control and 5 DicerloxP/loxP;Afp-Cre+ mice at P28.
Chips
  • Chip ID: GSM300676 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM300680 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM300678 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM300679 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM300677 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE12049

Experiment name Transcription profiling of mouse laminin alpha 2 chain deficient animals vs wild type [GSE12049]
Source GEO
Experiment description Mutations in the gene encoding laminin a2 chain cause congenital muscular dystrophy, MDC1A. In skeletal muscle, laminin a2 chain binds at least two receptor complexes; the dystrophin-glycoprotein complex and integrin a7b1. To gain insight into the molecular mechanisms underlying this disorder, we performed gene expression profiling of laminin a2 chain deficient mouse limb muscle. One of the down-regulated genes encodes a protein called calcium and integrin binding protein 2 (Cib2) whose expression and function is unknown. However, the closely related Cib1 has been reported to bind integrin aIIb and may be involved in outside-in-signaling in platelets. Since Cib2 might be a novel integrin a7b1 binding protein in muscle, we have studied Cib2 expression in the developing and adult mouse. Cib2 mRNA is mainly expressed in the developing central nervous system and in developing and adult skeletal muscle. In skeletal muscle Cib2 colocalizes with integrin a7B subunit at the sarcolemma and at the neuromuscular- and myotendinous junctions. Finally, we demonstrate that Cib2 is a calcium binding protein that interacts with integrin a7Bb1D. Thus, our data suggest a role for Cib2 as a cytoplasmic effector of integrin a7Bb1D signaling in skeletal muscle Experiment Overall Design: Skeletal muscle (all hind limb skeletal muscle) from 4-weeks old laminin alpha 2 chain deficient mice and 4-weeks old wild type mice were isolated individually and RNA were extracted and hybridized on Affiymetrix microarrys. Three biological replicates from each group were analyzed.
Chips
  • Chip ID: GSM304405 - Annotation by Bgee curators: Anatomical structure ID: MA:0000663 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM304404 - Annotation by Bgee curators: Anatomical structure ID: MA:0000663 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM304403 - Annotation by Bgee curators: Anatomical structure ID: MA:0000663 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE12769

Experiment name Transcription profiling of mouse postpartum testis developmental time course (0 to 35 day) [GSE12769]
Source GEO
Experiment description Murine testis developmental time course created from tissue samples collected from birth through adulthood and hybridized to M430_2 chips in duplicate. Experiment Overall Design: Time course of gene expression in the murine postpartum testis development (duplicates in day 0, 3, 6, 8, 10, 14, 18, 20, 30, 35). Total 20 samples.
Chips
  • Chip ID: GSM320306 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320305 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320304 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320307 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320312 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320311 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320308 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320313 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320309 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM320310 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE13402

Experiment name Transcription profiling of mouse SPARC-null vs. wild-type lens epithelium [GSE13402]
Source GEO
Experiment description SPARC is a matricellular glycoprotein involved in regulation of the extracellular matrix, growth factors, adhesion, and migration. SPARC-null mice have altered basement membranes and develop posterior sub-capsular cataracts with cell swelling and equatorial vacuoles. Exchange of fluid, nutrients, and waste products in the avascular lens is driven by a unique circulating ion current. Here we demonstrate that SPARC-null mouse lenses exhibit abnormal circulation of fluid, ion, and small molecules which leads to altered fluorescein distribution in vivo, loss of resting membrane polarization, and altered distribution of small molecules. Microarray analysis of SPARC-null lenses showed changes in gene expression of ion channels and receptors, matrix and adhesion genes, cytoskeleton, immune response genes, and cell signaling molecules. Our results demonstrate that the regulation of SPARC on cell-capsular matrix interactions can influence the circulation of fluid and ions in the lens, and the phenotype in the SPARC-null mouse lens is the result of multiple intersecting pathways. Experiment Overall Design: Lens epithelial cells from 7 lenses of littermate mice were isolated by laser capture microdissection. 3 wild-type lenses from 3 different mice and 4 knock-out lenses from 3 different mice were used as biological replicates.
Chips
  • Chip ID: GSM338339 - Annotation by Bgee curators: Anatomical structure ID: MA:0001301 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM338342 - Annotation by Bgee curators: Anatomical structure ID: MA:0001301 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM338341 - Annotation by Bgee curators: Anatomical structure ID: MA:0001301 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE13526

Experiment name Transcription profiling of mouse WT and Nxf2 KO post-natal day 21 testes [GSE13526]
Source GEO
Experiment description In euakryotes, mRNAs must be exported from the nucleus to the cytsoplasm. NXF2 is highly expressed in the mouse male germ cells. We are interested in its function in spermatogenesis, espically in the nuclear RNA export in the testis. To this end, we made Nxf2 mutant mice by gene targeting. In an attempt to identify the mRNA substrates of NXF2, we perform the microarray experiments on testes. We used microarrays to check the expression profiles of the Nxf2 WT and KO 21d testes on C57BL/6 background. Experiment Overall Design: To examine the expression difference between WT and Nxf2 KO testes, we collected testes from juvenile mice of three ages ( 21d, 26d, 28d). Testis weight was similar between WT and KO mice at post-natal day 21. Three pairs of WT and KO 21d testes were chosen for microarray analysis.
Chips
  • Chip ID: GSM341245 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM341246 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM341244 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE14242

Experiment name Transcription profiling of mouse WT and Hyp mice at 12 days of age reveals novel regulators of Fgf23 expression and mineralization in Hyp Bone [GSE14242]
Source GEO
Experiment description We used gene array analysis of cortical bone to identify Phex-dependent gene transcripts regulating Fgf23 production and mineralization in Hyp mice. We discovered that activation of Fgf receptor- and Wnt-pathways contribute to increased Ffg23 gene transcription in Hyp bone. We found evidence in Hyp bone for increased expression of Fgf1, Fgf7, and Egr2 in the Fgf-signaling pathway and decrements in Sost and Cpz and increments in Sfrp1 and 4 in the Wnt-signaling pathway. Moreover, activation of Fgf and Wnt-signaling stimulated, whereas Tgf inhibited Fgf23 promoter activity in osteoblasts. We also observed reductions in Bmp1, a metalloproteinase that metabolizes the Fgf23 regulatory extracellular matrix protein Dmp1. These findings suggest that elevation of Fgf23 expression in osteocytes is regulated by interactions between cell surface expression of Phex, extracellular matrix proteins and paracrine effects of Fgf and Wnt. Alterations were also found in enzymes regulating the posttranslational processing and stability of Fgf23, including decrements in the glycosyltransferase Galnt3 and the proprotein convertase Pcsk5. In addition, we found that the Pcsk5 and the glycosyltransferase Galnt3 were decreased in Hyp bone, suggesting that reduced post-translational processing of FGF23 may also contribute to increased Fgf23 levels in Hyp mice. With regards to mineralization, we identified additional candidates to explain the intrinsic mineralization defect in Hyp osteoblasts, including increases in the mineralization inhibitors Mgp and Thbs4, as well as increases in local pH altering factors, carbonic anhydrase 12 (Car12) and 3 (Car3) and the sodium-dependent citrate transporter (Slc13a5). These studies demonstrate the complexity of gene expression alterations in bone that accompanies inactivating Phex mutations and identify novel pathways that may coordinate Fgf23 expression and mineralization of extracellular matrix in Hyp bone. Experiment Overall Design: We isolated total RNAs from long bones of both WT and Hyp mice at 12 days of age. Since the RNA yields from the long bones are very low, we combined 2 bone samples with same genotype (WT or Hyp) for one RNA extraction. We will compare the difference of the gene expressions between Hyp and WT. We will use 4 samples in each animal condition.
Chips
  • Chip ID: GSM356756 - Annotation by Bgee curators: Anatomical structure ID: MA:0000300 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM356758 - Annotation by Bgee curators: Anatomical structure ID: MA:0000300 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM356757 - Annotation by Bgee curators: Anatomical structure ID: MA:0000300 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM356755 - Annotation by Bgee curators: Anatomical structure ID: MA:0000300 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE15452

Experiment name Expression data from lung of mice bearing mutations of FGFR3 and FGFR4 [GSE15452]
Source GEO
Experiment description Gene expression profiling of newborn lung tissue revealed few changes in compound FGFR3/FGFR4 deficient mice, consistent with their normal lung morphology at birth, suggesting the sequence of events leading to the phenotype initiates after birth in this model. Profiling of 4 week-old lung tissues revealed an induction of genes related to elastic fiber assembly in compound mutants. Lung RNA isolated from three animals of each genotype-age group were pooled for each Affymetrix chip (n=3 chips for each, except n=2 for wild type at 4 weeks.
Chips
  • Chip ID: GSM387656 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM387675 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM387657 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM387673 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM387674 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE16012

Experiment name Transcription profiling of mouse Elastin (Eln+/-) aorta and aortic valve tissue [GSE16012]
Source GEO
Experiment description Elastin wild type Eln+/+ and Eln+/- mouse aorta and aortic valve tissue. In the study, we demonstrated differential gene expression in juvenile elastin deficient mouse valve tissue. Experiment Overall Design: In the study, we hybridized RNA from Elastin wild type (Eln+/+) aorta tissue, elastin wild type (Eln+/+) aortic valve tissue, elastin (Eln+/-) aorta tissue and elastin (Eln+/-) aortic valve tissue to Affymetrix GeneChip Mouse Genome 430 2.0 Array
Chips
  • Chip ID: GSM400643 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM400649 - Annotation by Bgee curators: Anatomical structure ID: MA:0000087 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM400650 - Annotation by Bgee curators: Anatomical structure ID: MA:0000087 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM400651 - Annotation by Bgee curators: Anatomical structure ID: MA:0000087 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM400641 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM400642 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
  • Chip ID: GSM400652 - Annotation by Bgee curators: Anatomical structure ID: MA:0000087 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM400645 - Annotation by Bgee curators: Anatomical structure ID: MA:0000062 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE16114

Experiment name Transcription profiling of mouse 26-day-old K-ras conditional mutant mice and 3-month-old K-ras conditional mutant mice reveals cell-specific Kras and Pten mutations document proliferation arrest in granulosa cells vs. oncogenic insult to OSE cells [GSE16114]
Source GEO
Experiment description The small G-protein KRAS is crucial for mediating gonadotropin-induced events associated with ovulation. However, constitutive expression of KrasG12D in granulosa cells disrupted normal follicle development leading to the persistence of abnormal follicle-like structures containing non-mitotic cells. To determine what factors mediate this potent effect of KrasG12D, gene profiling analyses were done. We also analyzed KrasG12D;Cyp19-Cre and KrasG12D;Pgr-Cre mutant mouse models that express Cre prior to or after the initiation of granulosa cell differentiation, respectively. KrasG12D induced cell cycle arrest in granulosa cells of the KrasG12D;Cyp19-Cre mice but not in the KrasG12D;Pgr-Cre mice, documenting the cell context specific effect of KrasG12D. Expression of KrasG12D silenced the Kras gene, reduced cell cycle activator genes and impaired expression of granulosa cell and oocyte specific genes. Conversely, levels of PTEN and phosphorylated p38MAPK increased markedly in the mutant granulosa cells. Because disrupting Pten in granulosa cells leads to increased proliferation and survival, Pten was disrupted in the KrasG12D mutant mice. The Pten/Kras mutant mice were infertile but lacked GCTs. By contrast, the Ptenfl/fl;KrasG12D;Amhr2-Cre mice developed aggressive ovarian surface epithelial (OSE) cell tumors that did not occur in the Ptenfl/fl;KrasG12D;Cyp19-Cre or Ptenfl/fl;KrasG12D;Pgr-Cre mouse strains. These data document unequivocally that Amhr2-Cre is expressed in and mediates allelic recombination of oncogenic genes in OSE cells. That KrasG12D/Pten mutant granulosa cells do not transform but rather undergo cell cycle arrest indicates that they resist the oncogenic insults of Kras/Pten by robust self-protecting mechanisms that silence the Kras gene and elevate PTEN and phospho-p38MAPK. Experiment Overall Design: Whole ovaries were collected from 26-day-old wild type mice, 26-day-old K-ras conditional mutant mice and 3-month-old K-ras conditional mutant mice. The gene expression profiles of these samples were compared using microarray method.
Chips
  • Chip ID: GSM403221 - Annotation by Bgee curators: Anatomical structure ID: MA:0000384 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM403220 - Annotation by Bgee curators: Anatomical structure ID: MA:0000384 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE16585

Experiment name Transcription profiling of mouse retina from four genotypes: +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl at P14 and P28 [GSE16585]
Source GEO
Experiment description Rorb is essential for rod photoreceptor development in the mouse retina. Using Affymetrix mouse GeneChips, we have generated expression profiles of the +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl retina at P14 and P28. In this dataset, we include the expression data obtained from retina of wt and mutants. These data are used to obtain 1189 genes that are differentially expressed in Rorb-/- vs wt. Experiment Overall Design: 31 total samples were analyzed
Chips
  • Chip ID: GSM416869 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416870 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416871 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416885 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416884 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416886 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416887 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM416868 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE1830

Experiment name Transcription profiling of mouse spinal cord (L3-L5) between wild type and Egr3-deficient animals to identify spinal cord fusimotor neuron-specific genes [GSE1830]
Source GEO
Experiment description Egr3 is a zinc-finger transcription factor involved in growth and development. Egr3-deficient mice have severe sensory ataxia due to failed development of muscle spindle stretch receptors. Sensory and motor neurons that normally innervate spindles are absent in Egr3-deficient mice, presumably as a secondary consequence to the loss of trophic signals produced by spindles during development that are required for innervation and neuron survival. The molecular mechanisms involving motor neuron fate specification, target derived growth factor dependencies, and specification of target innervation have been difficult to study since select markers for functionally specific motor neurons are very poorly characterized. A more thorough understanding of the molecular mediators of motor neuron biology will be important to evaluate the efficacy of new strategies devised to thwart neuron death that occurs in a variety of human motor neuronopathies and neuropathies. To identify genes specifically expressed by spinal cord fusimotor neurons: Many motor neuron specific genes have been described over the years. However, none have been described that distinguish fusimotor neurons from skeletomotor neurons despite the fact that they have distinct muscle targets (muscle spindle stretch receptors) and comprise 25-30% of the spinal motor neuron populations. Since these motor neurons have remarkably different target innervation and function, we hypothesize that they express genes that establish their specific phenotypes during development. We hypothesize that fusimotor neurons can be distinguished in the spinal cord by characterizing fusimotor neuron specific gene expression. Once fusimotor neuron specific genes are identified, they will be used as markers to identify fusimotor neurons in complex neuroglial cell populations in vivo and in vitro. We hypothesize that by characterizing fusimotor neuron specific genes, unique marker molecules will be identified for in vivo and in vitro study of this functionally distinct and important motor neuron subtype. Moreover, we hypothesize that many of the genes that are specifically expressed by fusimotor neurons will be involved in mechanisms related to their fate specification, target innervation and growth factor dependent biology. We will use the Affymetrix microarray platform to identify genes that are specifically expressed by fusimotor neurons in mouse spinal cord. The differential expression analysis will be performed on microdissected segments of spinal cord (L3-L5) from wild type and Egr3-deficient mice. Postnatal Egr3-deficient mice lack muscle spindles and fusimotor neurons in their spinal cords. By comparing gene expression from microdissected segments of spinal cord (L3-L5) between wild type and Egr3-deficient mice, we hypothesize that fusimotor neuron selective genes can be identified. We will microdissect L3-L5 segments of spinal cord using precise anatomical landmarks to ensure that comparable spinal cord regions are anlayzed from each animal. For each microarray experiment, total RNA will be extracted from L3-L5 cords (approximately 2 mm length of spinal cord). The integrity of each RNA sample will be verified by gel electrophoresis. The intact RNA samples from mice of similar genotype will be pooled from three (3) 27-day old animals. The intact cord dissection is easier in young animals (eg: 27-day old) and the phenotype is known to exist at this developmental stage. The RNA from each animal of a similar genotype will be pooled into a single sample to minimize false positive gene calls that may represent genes related to the specific state of vigilance of a particular animal at the time of sacrifice (eg: activity dependent genes). Thus, each of the two RNA samples to be analyzed for a particular microarray experiment will represent RNA from three (3) spinal cords of each genotype. RNA amplification for probe synthesis should not be necessary since we will provide 7 ug of intact pooled total RNA for each sample. For statistical analysis, the experiment will be performed twice. Since the RNA samples are precious, they will be provided to the Array Consortium in two shipments with each of the experiments performed independently.
Chips
  • Chip ID: GSM32065 - Annotation by Bgee curators: Anatomical structure ID: MA:0000216 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: low quality

Affymetrix experiment GSE1835

Experiment name Transcription profiling of mouse retina response to myocilin. Russell-7U24NS043571-02 [GSE1835]
Source GEO
Experiment description Glaucoma is a neurodegenerative disease in which vision is lost as a result of the apoptosis of retinal ganglion cells. When the trabecular meshwork cells, that regulate aqueous humor outflow, are stressed as they are in some forms of glaucoma, they considerably up-regulated secretion of a protein called myocilin into the aqueous. The function of this protein is unclear; but since some aqueous humor flows to the posterior of the eye, the effects of myocilin will also be felt by the retinal cells. We have a transgenic mouse that secretes large amounts of myocilin into aqueous humor. In these mice, there is a deposition of myocilin on membranes of certain cells suggesting myocilin might have some signaling functions. This signaling function could explain why stresses that increase intraocular pressures can increase the likelihood for glaucoma, cause the myocilin to be secreted at very high levels by the trabecular meshwork. Myocilin may be important in treating glaucoma. This experiment will determine if myocilin is altering gene expression in the retina. The results should show variations in expression levels and will give us some indication of the pathways that are important to preserve retinal ganglion cells after a diagnosis of glaucoma. Our hypothesis is that myocilin is acting like a signaling protein in the eye. It acts not only in the anterior segment but also in retina as a result of the flow of some aqueous to the back of the eye. This signaling function is protective to certain ocular cells. This function of myocilin may influence cells in the retina and may counter the apoptotic signals in the retinal ganglion cells that occur during glaucoma. Retinas from transgenic mice and from mice of the same strain that do not have the transgene will be dissected. The mice will be three weeks of age. Because of the small size of the retina, samples will be pooled to obtain the RNA necessary to run the microarray. Three control and three transgenic samples will be run and compared with each other. We have data indicating that myocilin is at high levels in the aqueous humor of the transgenic animals.
Chips
  • Chip ID: GSM32153 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM32154 - Annotation by Bgee curators: Anatomical structure ID: MA:0000276 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE18567

Experiment name Temporal profiling of gene expression in cochleae of wild type and alpha9 null mice [GSE18567]
Source GEO
Experiment description Efferent inhibition of cochlear outer hair cells is mediated by nicotinic cholinergic receptors containing alpha9 (a9) and alpha10 subunits. Mice lacking a9 nicotinic subunits fail to exhibit classic olivocochlear responses and are characterized by abnormal synaptic morphology at the base of outer hair cells. To detail molecular changes induced upon the loss of a9 subunit, we sampled cochlear RNA from wild type and a9 null mice at postnatal (P) days spanning periods of synapse formation and maturation (P3, P7, P13 and P60). Our findings point to a delay in cochlear maturation starting at the onset of hearing (P13), as well as an up-regulation of various GABA receptor subunits in adult mice lacking the a9 nicotinic subunit. Cochleae were removed at postnatal ages P3, P7, P13 and P60. Cochlear tissues from 3-5 mice were pooled per replicate; biological triplicates were performed for each age and genotype.
Chips
  • Chip ID: GSM462021 - Annotation by Bgee curators: Anatomical structure ID: MA:0000239 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM462020 - Annotation by Bgee curators: Anatomical structure ID: MA:0000239 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM462019 - Annotation by Bgee curators: Anatomical structure ID: MA:0000239 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE18745

Experiment name S1P lyase deficiency disrupts lipid homeostasis in liver [GSE18745]
Source GEO
Experiment description The cleavage of sphingoid base phosphates by sphingosine-1-phosphate (S1P) lyase to produce phosphoethanolamine and a fatty aldehyde is the final degradative step in the sphingolipid metabolic pathway. We have studied mice with an inactive S1P lyase gene and have found that, in addition to the expected increase of sphingoid base phosphates, other sphingolipids (including sphingosine, ceramide, and sphingomyelin) were substantially elevated in the serum and /or liver of these mice. This latter increase is consistent with a reutilization of the sphingosine backbone for sphingolipid synthesis due to its inability to exit the sphingolipid metabolic pathway. Furthermore, the S1P lyase deficiency resulted in changes in the levels of serum and liver lipids not directly within the sphingolipid pathway, including phospholipids, triacyglycerol, diacylglycerol, and cholesterol. Even though lipids in serum and lipid storage were elevated in liver, adiposity was reduced in the S1P lyase-deficient mice. Microarray analysis of lipid metabolism genes in liver showed that the S1P lyase deficiency caused widespread changes in their expression pattern. These results demonstrate that S1P lyase is a key regulator of the levels of multiple sphingolipid substrates and reveal functional links between the sphingolipid metabolic pathway and other lipid metabolic pathways that may be mediated by shared lipid substrates and changes in gene expression programs. The disturbance of lipid homeostasis by altered sphingolipid levels may be relevant to metabolic diseases. Experiment Overall Design: RNA samples from liver for three sphingosine-1-phosphate lyase knock-out and three WT mice.
Chips
  • Chip ID: GSM465514 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM465512 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM465509 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE20954

Experiment name mRNA expression profile in mouse lung development [GSE20954]
Source GEO
Experiment description We performed miRNA and mRNA profiling over a 7-point time course, encompassing all recognized stages of lung development and explore dynamically regulated miRNAs and potential miRNA-mRNA interaction networks specific to mouse lung development replicated time course of mouse lung development in 7 time points
Chips
  • Chip ID: GSM523971 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM523970 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE21278

Experiment name A genomic atlas of mouse hypothalamic development [GSE21278]
Source GEO
Experiment description The hypothalamus is a central regulator of many behaviors essential for survival such as temperature regulation, food intake and circadian rhythms. However, the molecular pathways that mediate hypothalamic development are largely unknown. To identify genes expressed in developing mouse hypothalamus, microarray analysis at 12 different developmental time points was performed. Developmental in situ hybridization was conducted for 1,045 genes dynamically expressed by microarray analysis. In this way, we identified markers that stably labeled each major hypothalamic nucleus over the entire course of neurogenesis, and thus constructed a detailed molecular atlas of the developing hypothalamus. As proof of concept for the utility of this data, we used these markers to analyze the phenotype of mice where Sonic Hedgehog (Shh) was selectively deleted from hypothalamic neuroepithelium, demonstrating an essential role for Shh in anterior hypothalamic patterning. Our results serve as a resource for functional investigations of hypothalamic development, connectivity, physiology, and dysfunction. Affymetrix MOE430 microarrays were used to analyze the expression patterns of mouse hypothalamic and preoptic area tissues. The results were compared across the variables of Strain, Sex and Age.
Chips
  • Chip ID: GSM531855 - Annotation by Bgee curators: Anatomical structure ID: MA:0000173 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM531951 - Annotation by Bgee curators: Anatomical structure ID: MA:0000173 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM531950 - Annotation by Bgee curators: Anatomical structure ID: MA:0000173 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM531856 - Annotation by Bgee curators: Anatomical structure ID: MA:0000173 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE23081

Experiment name Identification of microRNA targets in the mammalian inner ear using a comprehensive transcriptome and proteome integrated approach [GSE23081]
Source GEO
Experiment description We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions using integrated miRNA, transcriptome and proteome profiles with advanced in silico analysis. By looking at both the transcript and protein levels of expression, a thorough coverage of miRNA regulation was obtained. Microdissected auditory and vestibular sensory epithelia were used as the model system, thus being the first time such a comparison was carried out in a neuroepithelial system. Moreover, this is one of only a few studies employing proteome screening for the identification of miRNA targets. Notably, this approach can be employed for the study of other tissues and organs. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. By searching for enrichment and depletion of miRNA targets in the transcript and protein datasets with a reciprocal or similar expression, respectively, as the regulatory miRNA, we identified functionally important miRNAs. Finally, the interaction between miR-135b and PSIP1-P75, a transcriptional coacitvator previously unknown in the inner ear, was identified and validated experimentally. We suggest that miR-135b may serve as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells. We investigated the mRNA expression profile of the cochlear and vestibular sensory epithelia from inner ears of postnatal day 2 mice using the Affymetrix GeneChip__ 430 2Mouse Genome array. Cochlear and vestibular sensory epithelia were dissected from wild type C3H mice and collected separately. The vestibular epithelia consisted of the saccule, utricle and the lateral and anterior cristae. Both the cochlear and vestibular sensory epithelia were dissected with their underlying mesenchyma. Altogether three pools, three biological replicates, of each tissue type were collected consisting of cochlear or vestibular sensory epithelia dissected from 10 to 12 inner ears.
Chips
  • Chip ID: GSM569093 - Annotation by Bgee curators: Anatomical structure ID: MA:0002892 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM569091 - Annotation by Bgee curators: Anatomical structure ID: MA:0000240 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM569092 - Annotation by Bgee curators: Anatomical structure ID: MA:0000240 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM569090 - Annotation by Bgee curators: Anatomical structure ID: MA:0000240 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM569094 - Annotation by Bgee curators: Anatomical structure ID: MA:0002892 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM569095 - Annotation by Bgee curators: Anatomical structure ID: MA:0002892 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE23845

Experiment name Time course for bladder UCC development in UPII-SV40Tag mice [GSE23845]
Source GEO
Experiment description We have identified genes that are differentially expressed between the bladders of UPII-SV40Tag mice and their age-matched wild-type littermates at 3, 6, 20, and 30 weeks of age. These are ages that correspond to premalignant, carcinoma in situ, and early-stage and later stage invasive UCC, respectively Analysis of the microarray data sets has revealed _1,900 unique genes differentially expressed (³3-fold difference at one or more time points) between wild-type and UPII-SV40Tag urothelium during the time course of tumor development. RNA from the urothelium of duplicate UPII-SV40Tag hemizygous and age-matched wild type littermate mice was isolated at 3, 6, 20, and 30 weeks of age and gene expression profiles were obtained.
Chips

Affymetrix experiment GSE23937

Experiment name Expression data from GNMT knockout mice cerebral cortex [GSE23937]
Source GEO
Experiment description We report that Gnmt-/- mice have abnormal behavior including spontaneous locomotion activity, PPI, TST and FST. Microarray analysis showed that genes expression profiles in male Gnmt -/- mice Keywords: Gnmt knockout Cerebral cortex tissues from wild-type or Gnmt knockout mice were used for RNA extraction and hybridization on Affymetrix microarrays. For 4 weeks old mice, total RNA were mixed in equal proportion from 3 mice.
Chips

Affymetrix experiment GSE24451

Experiment name Knockout of the Acyl CoA binding protein (ACBP) in mice - expression profile from the liver of 21 days old ACBP-/- and +/+ mice. [GSE24451]
Source GEO
Experiment description The ACBP knockout were created by targeted disruption of the gene in mice. The expression profiling was performed on liver tissue from ACBP-/- (KO) and +/+ (WT) mice at the age of 21 days, which in our study is the time immediately before weaning. The mice used for this experiment were taken directly away from their mother. Thus, having free access to chow and breast milk until sacrificed at 8-11am 15 ACBP-/- and 15 +/+ control mice divided into 6 groups (KO1, KO2, KO3, WT1, WT2 and WT3) with 5 individuals in each group were used for this study.
Chips
  • Chip ID: GSM602521 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM602522 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM602523 - Annotation by Bgee curators: Anatomical structure ID: MA:0000358 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE2463

Experiment name Transcription profiling of mouse wildtype and Foxn1::dnFGFR2-IIIb transgenic hair follicles [GSE2463]
Source GEO
Experiment description rationale: comparison of gene expression profiles in wildtype and Foxn1::dnFGFR2-IIIb transgenic hair follicles; identification of targets that mediate the effects seen in transgenic hair follicles; results: as already suggested by the phenotype, the molecular abnormalities appear to be restricted to the hair shaft medulla; Igfbp5 is an important mediator of transgene-dependent effects
Chips
  • Chip ID: GSM46551 - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality

Affymetrix experiment GSE25732

Experiment name Expression data from Pou4f3-Rb1 cKO and control inner ear [GSE25732]
Source GEO
Experiment description Retinoblastoma gene (Rb1) is required for proper cell cycle exit in the developing mouse inner ear and its deletion in the embryo leads to proliferation of sensory progenitor cells that differentiate into hair cells and supporting cells. In the Pou4f3-Cre:Rb1 flox/flox (Rb1 cKO) inner ear, utricular hair cells differentiate and survive into adulthood whereas differentiation and survival of cochlear hair cells are impaired. To comprehensively survey the pRb pathway in the mammalian inner ear, we performed microarray analysis of Rb1 cKO cochlea and utricle. P6 or 2-month control and Rb1 cKO littermates were euthanized and the inner ear tissues were dissected. Total RNA was extracted from the pooled samples. Technical duplicates of the pooled RNA were used for microarray.
Chips
  • Chip ID: GSM632078 - Annotation by Bgee curators: Anatomical structure ID: MA:0000247 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
  • Chip ID: GSM632081 - Annotation by Bgee curators: Anatomical structure ID: MA:0000240 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM632082 - Annotation by Bgee curators: Anatomical structure ID: MA:0000240 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM632077 - Annotation by Bgee curators: Anatomical structure ID: MA:0000247 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE26076

Experiment name Mouse conjunctival forniceal gene expression during postnatal development and its regulation by Kruppel-like factor 4 [GSE26076]
Source GEO
Experiment description Purpose: To identify the changes in postnatal mouse conjunctival forniceal gene expression and their regulation by Klf4 around eye opening stage when the goblet cells first appear. Methods: Laser-capture-microdissection was used to collect conjunctival forniceal epithelial cells from postnatal-day (PN) 9, PN14 and PN20 wild-type (WT), and PN14 Klf4-conditional null (Klf4CN) mice, where goblet cells are absent, developing, present, and missing, respectively. Microarrays were used to compare gene expression among these four groups. Expression of selected genes was validated by Q-RT-PCR, and spatiotemporal expression assessed by in situ hybridization. Results: We identified 668, 251, 1160 and 139 genes that were upregulated and 492, 377, 1419 and 57 genes that were downregulated between PN9 and PN14, PN14 and PN20, PN9 and PN20, and PN14 WT and Klf4CN conjunctiva, respectively. Transcription factors Spdef, FoxA1 and FoxA3 that regulate goblet cell development in other mucosal epithelia, and epithelial specific Ets (ESE) transcription factor family members were upregulated during conjunctival development. Mesenchymal-epithelial transition (MET) was favored and diverse pathways related to glycoprotein biosynthesis, mucosal immunity, signaling, endocytic and neural regulation were affected during conjunctival development. Conjunctival Klf4-target genes differed significantly from the previously identified corneal Klf4-target genes, implying tissue-dependant regulatory targets for Klf4. Conclusions: We have identified the changes in gene expression accompanying mouse conjunctival development and the role of Klf4 in this process. These studies provide new probes to study conjunctival epithelial development and function, and reveal that the gene regulatory network required for goblet cell development is conserved across different mucosal epithelia. Three independent samples in each of four developmental groups
Chips
  • Chip ID: GSM640276 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640282 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640280 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640274 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640278 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640275 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640277 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640279 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM640281 - Annotation by Bgee curators: Anatomical structure ID: MA:0000265 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE26745

Experiment name Comparison of total and polyribosome-associated mRNA levels in male Fmr1 KO mice and male WT littermates [GSE26745]
Source GEO
Experiment description The Fragile X Mental Retardation Protein, FMRP, is thought to regulate the translation of a specific set of neuronal mRNAs on polyribosomes. Therefore, we prepared polyribosomes on sucrose gradients and purified mRNA specifically from these fractions, as well as the total mRNA levels, to determine whether a set of mRNAs might be changed in its % association with polyribosomes in the absence of FMRP in the KO mouse model. No significant differences were found, other than the Fmr1 transcript itself, in total mRNA levels or % polyribosome association that withstood multiple test correction, in P7 Fmr1 KO mouse cerebral cortex compared with WT littermates.. We prepared polyribosomes on sucrose gradients from 6 littermate pairs of Fmr1 KO and WT littermates (FVB background, P7 males, cerebral cortex) and purified RNA from both polyribosomal fractions and input to the gradient, reflecting total mRNA levels for comparison.
Chips
  • Chip ID: GSM658274 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM658270 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM658272 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM658273 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM658271 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM658269 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE27568

Experiment name Ubb Knockout Mouse Testis [GSE27568]
Source GEO
Experiment description Analysis of Ubb knockout mouse testes at 7, 4, 21, and 28 dpp. Ubiquitin (Ub) is an essential protein found in all eukaryotic cells and plays important roles in a variety of cellular functions including germ cell development. Targeted disruption of the polyubiquitin gene Ubb results in male and female infertility in mice with germ cells arrested at meiotic prophase I. Whole testes from wild-type (WT) and Ubb-/- (KO) mice were harvested at 7, 14, 21, and 28 days postpartum. Total RNA was extracted and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.
Chips
  • Chip ID: GSM682305 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682309 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682312 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682304 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682317 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682308 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682316 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM682313 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE28025

Experiment name Comparative gene expression analysis of repro9/repro9 and wild type testes from 14 and 17 day mice [GSE28025]
Source GEO
Experiment description Repro9 in an allele of Mybl1 (A-Myb) transcription factor obtained in ENU screen to identify alleles causing mouse infertility. Repro9/repro9 mutant males are infertile due to meiotic arrest at pachytene stage. Mutants show wide range of abnormalities including inefficient chromosome synapsis, sex body formation and progression through meiotic cycle. Females are unaffected. To determine genes transcriptionally regulated by MYBL1 we analyzed gene expression profiles of wild type and repro9/repro9 mutant testis at 14 and 17 days postpartum. Analysis revealed many misregulated genes, in majority downregulated, at day 14 pp and even more at day 17 pp, probably due to secondary effects of meiotic arrest. Significantly misregulated genes were characterized by Gene Ontology. Comparative gene expression analysis uncovered potential targets of MYBL1 regulation that play roles in regulation of transcription, cell cycle, apoptosis, protein phosphorylation and ubiquitination, chromosome organization and others. Abstract:The transcriptional regulation of mammalian meiosis is poorly characterized, due to few genetic and ex vivo models. From a genetic screen, we identify the transcription factor MYBL1 as a male-specific master regulator of several critical meiotic processes. Spermatocytes bearing a novel separation-of-function allele (Mybl1repro9) had subtle defects in autosome synapsis in pachynema, a high incidence of unsynapsed sex chromosomes, incomplete double strand break (DSB) repair on synapsed pachytene chromosomes, and a lack of crossing-over. MYBL1 protein appears in pachynema, and its mutation caused specific alterations in expression of diverse genes, including some translated postmeiotically. These data, coupled with chromatin immunoprecipitation (ChIP-chip) experiments and bioinformatic analysis of promoters, identified direct targets of MYBL1 regulation. Meiosis in mutant females appears unaffected. These results reveal that MYBL1 is a master regulator of meiotic genes that are involved in multiple processes in spermatocytes, including chromosome synapsis, recombination, and cell cycle progression through pachynema. RNA was extracted from wt and repro9/repro9 mutant testis from 14 and 17 days old mice. This two time points were selected for sample enrichment in early/midpachytene and latepachytene/diplotene spermatocytes, respectively. Total testis RNA from wild-type (³3) and mutant (³3) mice was reverse-transcribed into double stranded cDNA, and biotin-labeled cRNA (GeneChip IVT labeling kit, Affymetrix, Santa Clara, CA) was hybridized to Affymetrix mouse genome 430 2.0 GeneChips containing. The raw data was processed using Affymetrix GCOS software. Two-way ANOVA analysis resolved differentially expressed (DE) genes either between genotypes and/or days using MeV(version 4.6.1) on log2-transformed expression values. Results were multiple test corrected with the Benjamini-Hochberg method to control the false discovery rate (FDR) in R. ~800 genes significant at FDR<=0.025 were selected as differentially expressed for downstream analysis.
Chips
  • Chip ID: GSM692971 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM692977 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM692969 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM692970 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE28664

Experiment name Akt1 is critical in Maintaining the Blood-Testis Barrier Following Exposure to the Neonatal Goitrogen, 6-N-Propylthiouracil (PTU) [GSE28664]
Source GEO
Experiment description Akt1 plays a protective role in the postnatal C57BL6 mouse testis following lactational exposure to the neonatal goitrogen, propylthiouracil (PTU). To elucidate the transcriptional profile mediating this phenotypic effect, we monitored changes in testicular gene expression at postnatal days (PNDs) 15 and 25 in Akt1+/+, Akt1+/-, and Akt1-/- testes following exposure to 0.01% PTU allowing us to determine changes in gene expression due to 1.) genotype effects; 2.) exposure effects; and 3.) genotype-by-exposure interactions. Early PTU-dependent gene changes included genes involved in lipid metabolism, spermatid differentiation, meiosis and adhesion. Early Akt1-dependent effects were associated with germ cell development, spermatid development and differentiation, and sperm motility. By PND25, the Akt1 gene-environment interaction had pronounced effects on genes associated with Sertoli cell (SC) differentiation and claudin-associated junctional formation suggesting delayed formation of the blood-testis barrier (BTB). To confirm these observations, biotin tracer experiments demonstrated a permeable blood-testis barrier in PTU-exposed PKBalpha/Akt1-/- tubules as late as PND25 compared to PTU-exposed Akt1+/+ seminiferous tubules. Transmission electron microscopy demonstrated altered SC morphology, aberrant SC localization, and disorganized actin bundle formation. Taken together, loss of Akt1 coupled with postnatal exposure to the neonatal goitrogen, PTU, in the testis contributes to a transcriptional profile associated with impaired integrity of the blood-testis barrier. In summary, the Akt1-/- mouse represents a potentially important model to study BTB formation and reassembly in response to male reproductive toxicants and the various signaling networks which mediate these responses. The microarray analysis employed a balanced factorial design, with one chip created for each of three mice under each experimental condition: mouse genotype (Akt1+/+, Akt1+/-, and Akt1-/-), exposure (PTU and Control), and age (sacrificed at PND15 and 25), with a total of 36 mice and 36 chips. MoGene 1.0 st v1 arrays were used for the samples from PND 15 and Mouse Genome 430 2.0 arrays were used for the samples from PND 25. One chip, PTU-exposed, Akt1-/-, PND25, was determined to not be of high quality and was not included in the analysis or provided here.
Chips
  • Chip ID: GSM710033 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM710034 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM710035 - Annotation by Bgee curators: Anatomical structure ID: MA:0000411 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE2873

Experiment name Transcription profiling of mouse skeletal muscle to detect genes that regulate motor axon growth and differentiation [GSE2873]
Source GEO
Experiment description These experiments are designed to discover genes that are expressed selectively by synaptic nuclei in skeletal muscle with the particular goal of identifying genes that regulate motor axon growth and differentiation. We plan to isolate RNA from the dissected synaptic region of skeletal muscle and from the non-synaptic region of skeletal muscle and to identify the genes that are expressed at higher levels in the synaptic than non-synaptic region. Previously, we showed that motor axons fail to stop and differentiate in mice lacking MuSK, a receptor tyrosine kinase that is activated by motor neuron-derived Agrin. We hypothesize that MuSK activation normally leads to the production of a retrograde stop/differentiation signal that is encoded by a gene that is expressed preferentially in synaptic nuclei. In the absence of MuSK signaling, the retrograde signaling is not produced by synaptic nuclei, and consequently motor axons wander aimlessly over the muscle. We obtain 6 to 8 micrograms of total RNA from the dissected synaptic or non-synaptic region from a single P21 mouse diaphragm muscle. This is a standard procedure in the lab, and we have used these methods to analzye gene expression and to generate high-quality cDNA libraries. Because the synaptic zone is narrower in the left hemi-diaphragm, we will isolate RNA from this half of the diaphragm. In order to isolate sufficient RNA (5 micrograms from each sample), we will pool the synaptic and non-synaptic regions from two hemi-diaphragms. In order to reduce experimental variability, we wish to analzye expression in six samples: three samples of synaptic RNA and three samples of non-synaptic RNA. We will ship the isolated RNA samples to the Consortium in order to generate labeled cDNA, to screen Affymetrix mouse oligo arrays and to assist in the analysis. Several genes, including the subunits of the acetylcholine receptor, MuSK, acetylcholinesterase, and utrophin are known to be expressed preferentially in synaptic nuclei; thus, these genes serve as internal controls for the reliability and effectiveness of the screen. Most other genes, several of which we have analyzed in previous studies, including actin, GAPDH, runx1, nogoC, creatine kinase, etc. are expressed uniformly in skeletal muscle; thus, expression of these genes should be equally represented in synaptic and non-synaptic regions. Experiment Overall Design: as above
Chips
  • Chip ID: GSM53238 - Annotation by Bgee curators: Anatomical structure ID: MA:0001904 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM53239 - Annotation by Bgee curators: Anatomical structure ID: MA:0001904 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM53236 - Annotation by Bgee curators: Anatomical structure ID: MA:0001904 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM53237 - Annotation by Bgee curators: Anatomical structure ID: MA:0001904 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE29081

Experiment name Cerebellar gene expression analysis of Gb5-deficient mice [GSE29081]
Source GEO
Experiment description Gb5 is a divergent, evolutionarily-conserved, member of the heterotrimeric G protein b subunit family that is expressed principally in brain and neuronal tissue. Among Gb isoforms, Gb5 is unique in its ability to heterodimerize with members of the R7 subfamily of the regulator of G protein signaling (RGS) proteins that contain G protein-g like (GGL) domains. Previous studies employing Gb5 knockout mice have shown that Gb5 is an essential stabilizer of GGL domain-containing RGS proteins and regulates the deactivation of retinal phototransduction and the proper functioning of retinal bipolar cells. The purpose of this study is to better understand the functions of Gb5 in the brain outside the visual system by employing molecular biology, immunohistochemistry and confocal imaging technologies. We show here that mice lacking Gb5 have a markedly abnormal neurologic phenotype that includes neurobehavioral developmental delay, wide-based gait, motor learning and coordination deficiencies, and hyperactivity. Using immunohistochemical analysis and a green fluorescent reporter of Purkinje cell maturation we show that the phenotype of Gb5-deficient mice includes, in part, delayed development of the cerebellar cortex, an abnormality that likely contributes to the neurobehavioral phenotype. Multiple neuronally-expressed genes are dysregulated in cerebellum of Gb5 KO mice. Brain tissues from WT and KO with three biological replications of mice were collected, frozen in liquid nitrogen, and stored at -70 C
Chips
  • Chip ID: GSM720605 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM720604 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM720606 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE29082

Experiment name Gene expression analysis of non-cerebellar portion of Gb5-deficient mice brain [GSE29082]
Source GEO
Experiment description Gb5 is a divergent, evolutionarily-conserved, member of the heterotrimeric G protein b subunit family that is expressed principally in brain and neuronal tissue. Among Gb isoforms, Gb5 is unique in its ability to heterodimerize with members of the R7 subfamily of the regulator of G protein signaling (RGS) proteins that contain G protein-g like (GGL) domains. Previous studies employing Gb5 knockout mice have shown that Gb5 is an essential stabilizer of GGL domain-containing RGS proteins and regulates the deactivation of retinal phototransduction and the proper functioning of retinal bipolar cells. The purpose of this study is to better understand the functions of Gb5 in the brain outside the visual system by employing molecular biology, immunohistochemistry and confocal imaging technologies. We show here that mice lacking Gb5 have a markedly abnormal neurologic phenotype that includes neurobehavioral developmental delay, wide-based gait, motor learning and coordination deficiencies, and hyperactivity. Using immunohistochemical analysis and a green fluorescent reporter of Purkinje cell maturation we show that the phenotype of Gb5-deficient mice includes, in part, delayed development of the cerebellar cortex, an abnormality that likely contributes to the neurobehavioral phenotype. Multiple neuronally-expressed genes are dysregulated in non-cerebellar portion of Gb5 KO mice. Brain tissues(non-cerebellar portion of brain) from WT and KO with three biological replications of mice were collected, frozen in liquid nitrogen, and stored at -70 C
Chips
  • Chip ID: GSM720614 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM720615 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM720613 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE31199

Experiment name Down-regulation of cholesterol biosynthesis in forebrains of ERCC1-deficient mice [GSE31199]
Source GEO
Experiment description Background: Several genetic defects of the nucleotide excision repair (NER) pathway, including deficiency of the Excision Repair Cross-Complementing rodent repair deficiency, complementation group 1 (ERCC1), result in pre-mature aging, impaired growth, microcephaly and delayed development of the cerebellum. Such a phenotype also occurs in ERCC1-knockout mice which survive for up to 4 weeks after birth. Therefore, we analyzed cerebellar and hippocamapal transcriptomes of these animals at 3 weeks of age to identify the candidate mechanisms underlying brain consequences of reduced ERCC1 activity. Results: In the cerebellum, the most prominent change was upregulation of genes that are associated with gliosis. Although Purkinje cell degeneration has been reported in some mouse strains with NER impairment, Purkinje cell transcriptome was mostly unaffected by the ERCC1 knockout. In the hippocampus, the gliosis response was minimal. Instead, there was an extensive downregulation of genes related to lipid metabolism including several enzymes of the cholesterol biosynthesis pathway as well as lipoproteins and plasma membrane proteins. Reduced expression of the cholesterol biosynthesis pathway genes was also present in the neocortex of adult mice whose ERCC1 gene was replaced by a mutant allele with a partial activity. Conclusions: Downregulation of forebrain cholesterol biosynthesis genes is a newly identified consequence of ERCC1 deficiency. Its presence in adult mice suggests that it is not a secondary consequence of brain growth impairment. Instead, reduced cholesterol biosynthesis may contribute to such an impairment as well as affect function of mature synapses. We analyzed the hippocampus and cerebellum from three Ercc1-/- and three WT littermates using the Affymetrix Mouse Genome 430_2.0. Data was analyzed using the dChip DNA-Chip analyzer software .
Chips

Affymetrix experiment GSE34051

Experiment name Expression profiling of the early postnatal stage of Polycystic Kidney Disease in the B6C3Fe a/a-bpck mice [GSE34051]
Source GEO
Experiment description To understand the molecular and cellular mechanisms of pathogenesis of autosomal recessive polycystic kidney disease , we performed a microarray gene expression profiling in early stage kidneys of B6C3Fe a/a-bpck mutant and wild-type mice at postnatal day 3. Genes with over 1.5-fold expression changes in mutant kidneys compared with age matched wild-type tissues were selected for analysis. This study represents the first widespread profiling of B6C3Fe a/a-bpck mutant mouse kidney and provides a valuable platform for better understanding the molecular mechanisms of polycystic kidney disease in human. Mutational analysis was performed in accordance with the protocol of Jackson Laboratory, total RNA was extracted from kidneys of 3 days of postnatal age using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol reagent (Invitrogen) according to their manual, and the samples were incubated with RNase-free DNase I (Ambion). The quality and concentration of each sample were confirmed by spectrophotometry. Affymetrix 430 2.0 arrays were used according to standard Affymetrix procedures. Data analysis was performed with dChip software (Dec.2010 version). These measurements were confirmed by Real-Time PCR.
Chips
  • Chip ID: GSM841006 - Annotation by Bgee curators: Anatomical structure ID: MA:0000368 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE4537

Experiment name Transcription profiling of mouse primary visual cortext from animals treated with monocular deprivation (MD), dark rearing and controls reveals binding protein of Insulin-like Growth Factor 1 is highly upregulated after MD [GSE4537]
Source GEO
Experiment description Two key paradigms for examining activity-dependent development of primary visual cortex (V1) involve either reduction of activity in both eyes via dark-rearing (DR) or imbalance of activity between the two eyes via monocular deprivation (MD).,Combining DNA microarray analysis with computational approaches, RT-PCR, immunohistochemistry and physiological imaging, we find that DR leads to (i) upregulation of genes subserving synaptic transmission and electrical activity, consistent with a coordinated response of cortical neurons to reduction of visual drive, and (ii) downregulation of parvalbumin, implicating parvalbumin-expressing neurons as underlying the delay in cortical maturation after DR. MD partially activates homeostatic mechanisms but differentially upregulates gene systems related to growth factors and neuronal degeneration, consistent with reorganization of connections after MD. A binding protein of Insulin-like Growth Factor 1 is highly upregulated after MD, and exogenous application of IGF1 prevents the physiological effects of MD on ocular dominance plasticity examined in vivo.
Chips

Affymetrix experiment GSE4752

Experiment name Transcription profiling of mouse cerebral cortext from Egr1/3 double knockout vs. wild type [GSE4752]
Source GEO
Experiment description The early growth response (Egr) family of transcriptional regulators consists of four closely related molecules (Egr1-4) that regulate target genes involved in cellular growth and differentiation. In the brain, Egr transcription factors have a critical role in learning and memory processing, presumably by regulating effector target genes that alter synaptic efficacy or mediate structural changes in neurons. Previous work suggests that Egr1 and Egr3 are the most important synaptic activity induced Egr molecules in the brain and they appear to have redundant regulatory function. How Egr transcriptional regulators influence learning and memory processing in the brain is unknown because target genes regulated by them have not been identified. Using Affymetrix microarray analysis and Egr loss-of-function mice, we will begin to characterize the gene regulatory networks modulated by Egr transcription factors in the brain. We anticipate that basic mechanisms related to transcriptional control of learning and memory related plasticity and the identification of plasticity effector molecules that may be involved in synaptic dysfunction associated with degenerative diseases or brain injury will result from these studies. To identify Egr transcription factor target gene regulation in brain: Target genes regulated by Egr transcription factors have not been identified in the brain, yet the transcription factors are essential for normal learning and memory processes. Using Egr1/3 double knockout and wild type littermate mice, we will compare gene expression profiles from somatosensory cortex to identify genes that are deregulated in Egr1/3 dKO brains. Egr1 and Egr3 gene expression is coupled to synaptic N-methyl D-aspartate (NMDA) receptor activation, mitogen activated protein kinase (MAPK) signaling engaged by NMDA receptor activation and long term synaptic potentiation (LTP). Previous studies have demonstrated defects in late phase LTP, long-term memory in hippocampal dependent tasks and reconsolidation of memories in Egr1-deficient mice, but the target effector molecules regulated by Egr transcription factors are not known. We hypothesize that it will be possible to identify Egr dependent target genes by using Affymetrix microarray analysis to compare gene expression from wild type cerebral cortex that has high levels of Egr protein expression with gene expression in cortex from Egr1/3 double knockout mice. Egr1 and Egr3 are highly expressed in mouse cortex and hippocampus twenty one days after birth because of the large amount of maternal stimulation they receive prior to weaning. We will compare the gene expression profile in somatosensory cortex from P21 wild type mice to that of P21 Egr1/3 dKO mice. We will perform microarray analysis using the Mouse 430 2.0 gene array with RNA samples from 3 wild type and 3 1/3 dKO brains (6 arrays total). Differentially regulated genes (up-regulated and down-regulated) will be identified from the list of genes with significantly altered expression greater than or equal to 2-fold by paired T test. Interesting genes will be validated by real-time PCR in wild type and 1/3 dKO brains. Our main goal is to identify genes that are directly regulated by Egr3. Recognizing that both direct and indirect target genes may be identified in the list of differentially expressed genes, real-time PCR validated target genes will be further screened using chromatin immunoprecipitation coupled with PCR (ChIP-PCR) to determine whether Egr1 and/or Egr3 are bound to potential regulatory regions of the putative target genes.
Chips
  • Chip ID: GSM107466 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM107464 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM107465 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE6310

Experiment name Brain BRCA1 conditional knockout [GSE6310]
Source GEO
Experiment description BRCA1 nestin CRE conditional knockout cortrices of P7 animals were compared to wildtype littermates to characterize the mutant phenotype. Keywords: expression BRCA1 conditional knockouts using nestin CRE and a null allele with an inverted neo cassette at the 5' end of the exon 11 of BRCA1 on one floxed allele flanking exons 5-13. Cortices of 3 wildtype animals were compred to 3 BRCA cKO at postnatal day 7.
Chips
  • Chip ID: GSM149216 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
  • Chip ID: GSM149215 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
  • Chip ID: GSM149221 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM149214 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM149210 - Annotation by Bgee curators: Anatomical structure ID: MA:0000185 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM149220 - Annotation by Bgee curators: Anatomical structure ID: MA:0000168 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: absent - Quality: high quality

Affymetrix experiment GSE640

Experiment name Transcription profiling of mouse testises at different developmental stages and cultures enriched in mouse Sertoli or interstitial cells to identify genes expressed differentially in meiotic or postmeiotic spermatogenic cells. [GSE640]
Source GEO
Experiment description A multitude of genes expressed solely in meiotic or postmeiotic spermatogenic cells offers a myriad of contraceptive targets. Understanding mammalian spermatozoan development and the events surrounding fertilization has grown slowly, in part because of uncertainty about the number and identity of the cellular components involved. Determination of those transcripts expressed specifically by germ cells should provide an inclusive list of probable critical proteins. Here, total mouse testis transcript profiles were trimmed of transcripts found in cultures enriched in Sertoli or interstitial cells to yield a germ cell-enriched transcript profile. Monitoring of changes of this profile in the developing testis identified 1,652 genes whose transcript abundance increased markedly coincident with the onset of meiosis. Remarkably, 351 of these genes ( approximately 20%) appear to be expressed only in the male germline. Germ cell-specific transcripts are much less common earlier in testis development. Further analysis of the UniGene EST database coupled with quantitative PCR indicates that approximately 4% of the mouse genome is dedicated to expression in postmeiotic male germ cells. Most or many of the protein products of these transcripts are probably retained in mature spermatozoa. Targeted disruption of 19 of these genes has indicated that a majority have roles critical for normal fertility. Thus, we find an astonishing number of genes expressed specifically by male germ cells late in development. This extensive group provides a plethora of potential targets for germ cell-directed contraception and a staggering number of candidate proteins that could be critical for fertilization.
Chips

Affymetrix experiment GSE6867

Experiment name Transcription profiling of mouse Notch1 deficient in hair follicles [GSE6867]
Source GEO
Experiment description Notch1 deficient hair matrix keratinocytes have lower mitotic rates, resulting in smaller follicles with fewer cells. In addition, the ratio of melanocytes to keratinocytes is greatly reduced. Microarray was performed to study downstream mechanism of Notch1-deficiency Experiment Overall Design: Microarray was first performed using HF_emN1-1 and HF_anN1-1 samples. Later, HF_emN1-2, HF_anN1-2, HF_WT-1, and HF_WT-2 were used to perform another set of microarray. anN1s and WTs were used as wild-type controls.
Chips
  • Chip ID: GSM158363 - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM158362 - Annotation by Bgee curators: Anatomical structure ID: MA:0000154 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE7310

Experiment name Transcription profiling of mouse C57BL6J lung exposed to 2 weeks of cigarette smoke compared to age-matched controls [GSE7310]
Source GEO
Experiment description We hypothesize that gene expression in the cigarette smoke (CS) exposed neonatal lung and age-matched controls will be divergent. CS exposed lung will have divergence of immune response genes and structural genes. The lungs of (6) 2 week old neonatal mice exposed to 2 weeks of CS were compared to the lung of (4) 2 week old age-matched control mice. We utilized microarray analysis to examine transcriptional differences between smoke exposed neonatal lung and age-matched controls. Experiment Overall Design: This study utilizes microarray analysis to test these hypotheses. Six sets of lungs were harvested from CS exposed mice and four sets of lungs were harvested from age-matched control mice. RNA was isolated and used for global gene expression profiling (Affymetrix Mouse 430 2.0 array). Statistically significant gene expression was determined as a minimum 6 counts of 9 pairwise comparisons, minimum 1.5-fold change, and p < 0.05. Further, Absolute | FC - FC SEM | >= 1.5.
Chips
  • Chip ID: GSM176495 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM176496 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM176498 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM176497 - Annotation by Bgee curators: Anatomical structure ID: MA:0000415 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE7333

Experiment name Transcription profiling of mouse hearts from wild type and miRNA-1-2 knockout mutants at postnatal day 10 to provide insight into the role of miRNA-1-2 in cardiac development [GSE7333]
Source GEO
Experiment description Microarray was done on heart tissue from ko and wt; MicroRNAs (miRNAs) are genomically encoded small RNAs used by organisms to regulate the dosage of proteins generated from messenger RNA transcripts. The in vivo requirement of specific miRNAs in mammals is unknown, and reliable prediction of mRNA targets remains problematic. Here, we show that miRNA biogenesis in the mouse heart is essential for cardiogenesis. Furthermore, targeted deletion of the muscle-specific miRNA, miR-1-2, revealed numerous functions in the heart, including regulation of cardiac morphogenesis, electrical conduction, and cell cycle control. Analyses of miR-1 complementary sequences in mRNAs upregulated upon miR-1-2 deletion revealed an enrichment of miR-1 seed matches" and a strong tendency for potential miR-1 binding sites to be located in physically accessible regions. These findings indicate that subtle alteration of miRNA dosage can have profound consequences in mammals and demonstrate the utility of mammalian loss-of-function models in revealing physiologic miRNA targets. Experiment Overall Design: Heart tissues from 3 wild type and 3 miR-1-2 knockout mice at postnatal days 10 were used and total RNA was extracted by Trizol. Expression level was compared between wild type and miR-1-2 knockout mice. The affy package from R/Bioconductor was used to generate RMA values.
Chips
  • Chip ID: GSM176758 - Annotation by Bgee curators: Anatomical structure ID: MA:0000072 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM176759 - Annotation by Bgee curators: Anatomical structure ID: MA:0000072 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM176756 - Annotation by Bgee curators: Anatomical structure ID: MA:0000072 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE7657

Experiment name Transcription profiling of mouse model of rheumatoid arthritis - identification of phase-specific arthritis-related genes in mice [GSE7657]
Source GEO
Experiment description Rheumatoid arthritis (RA), one of the most common polygenic diseases, is characterized by a chronic, progressive inflammation mainly in joints and has an unknown etiology. Numerous studies have revealed the significance of cytokines TNF and IL-1 in the onset and progression of RA. Due to the complexity of interactions among different cytokines and immune cells, little is known about the precise molecular mechanisms underlying RA. In this study, oligonucleotide microarray analysis and a mouse model of RA, IL-1 receptor antagonist deficient mice were used to address this issue. Two hundred and ninety transcripts were found to be dysregulated greater than or equal to 2-fold in the diseased mice. Phase-specific gene expression changes were identified, including early increase and late decrease of heat shock protein coding genes and Cyr61. Moreover, common gene expression changes were also observed, especially the upregulation of paired-Ig-like receptor A (Pira) in both early and late phases of arthritis. We conclude that common and distinct gene expression change patterns that were identified globally may represent novel opportunities for better control of RA through early diagnosis and development of alternative therapeutic strategies. Experiment Overall Design: Six wild-type and 6 Il1rn deficient BALB/c mice at 1 month and 4 month (3 for each time point) were used for microarray analysis of splenic gene expression profiling.
Chips
  • Chip ID: GSM185029 - Annotation by Bgee curators: Anatomical structure ID: MA:0000141 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM185030 - Annotation by Bgee curators: Anatomical structure ID: MA:0000141 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM185031 - Annotation by Bgee curators: Anatomical structure ID: MA:0000141 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE8065

Experiment name Transcription profiling of mouse small intestine at postnatal days 4,7,9,11,24 to investogate postnatal development of the small intestine [GSE8065]
Source GEO
Experiment description It was the purpose to analyse the changes in gene expression which occur in the mouse small intestine from the pre-weaning to the post-weaning stage. The gene expression was accordingly followed from postnatal day 4 to postnatal day 32. Experiment Overall Design: 6 time-points were defined corresponding to postnatal day 4, 7, 9, 11, 24 and 32. Ileal samples were taken from individual mice at each time-point. All layers of the small intestine were included in the sample. Three samples from individual mice were analysed by hybridization to Affymetrix GeneChips.
Chips
  • Chip ID: GSM198941 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198882 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198884 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: marginal - Quality: low quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198879 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198881 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198878 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198883 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198880 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM198885 - Annotation by Bgee curators: Anatomical structure ID: MA:0000339 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE8249

Experiment name Transcription profiling of mouse Foxo3 mutant ovaries vs. wild types to discover and classify ovarian fertility factors. [GSE8249]
Source GEO
Experiment description Female infertility syndromes are among the most prevalent chronic health disorders in women, but their molecular basis remains unknown because of the complexity of oogenesis and uncertainty regarding the number and identity of ovarian factors controlling the assembly, preservation, and maturation of ovarian follicles. To systematically discover such ovarian fertility factors en masse, we employed a mouse model (Foxo3), where follicles are assembled normally but are then synchronously activated. Gene expression profiling of mutant and normal ovaries led to the identification a surprisingly large set of ovarian factors. The set included the vast majority of known ovarian factors, many of which when mutated produce female sterility phenotypes, but most were novel. Subsequent analyses revealed novel classes of ovarian factors and significant overrpresentation on the X chromosome, among other insights into the general properties of oogenesis genes and their patterns of expression. Experiment Overall Design: Total ovarian RNA from +/+ and -/- ovaries at PND1, 3, 7, and 14 (n=3 replicates per timepoint and genotype, a total of 24 microarrays) was subjected to linear RNA amplification and hybridized to Affymetrix 430 2.0 mouse whole-genome microarrays, which interrogate >39K transcripts including the vast majority of protein-coding genes. We also profiled 14 somatic tissues. Additionally, to provide more refined views of gene expression, we profiled adult ovaries, adult testis, KitlSl/KitlSl-d testis (devoid of germ cells except for rare spermatogonia) (Shinohara et al., 2000), ES cells, laser-capture microdissected (LCM) primary oocytes, LCM somatic cells (granulosa cells + surrounding stroma), superovulated unfertilized eggs, cumulus granulosa cells, and E11 Foxo3 +/+ and -/- embryos. Each array data set was independently normalized by global median scaling, and the signal strengths were averaged for those samples for which replicates were available (PND1-14).
Chips
  • Chip ID: GSM204028 - Annotation by Bgee curators: Anatomical structure ID: MA:0001707 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM204048 - Annotation by Bgee curators: Anatomical structure ID: MA:0000388 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM203831 - Annotation by Bgee curators: Anatomical structure ID: MA:0000384 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM203832 - Annotation by Bgee curators: Anatomical structure ID: MA:0000384 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE8307

Experiment name Transcription profiling of prosaposin deficient mice show molecular alterations precede neuronal deficits [GSE8307]
Source GEO
Experiment description Prosaposin encodes, in tandem, four small acidic activator proteins (saposins) with specificities for glycosphingolipids hydrolases in lysosomes. To explore the molecular mechanism(s) of disease progression, temporal transcriptome microarray analyses of cerebrum and cerebellum tissues were conducted using mRNA from three prosaposin deficiency mouse models: PS-NA (hypomorphic prosaposin deficiency), PS-/- (prosaposin null) and 4L/PS-NA (a V394L/V394L glucocerebrosidase mutation and PS-NA) mice. Our results indicate that regionally specific gene expression abnormalities preceded the histological and behavioral changes and CEBPD is a candidate regulator of brain disease in prosaposin deficiency. The alterations of gene expression are detected at birth and are more profound in cerebellum than cerebrum. Experiment Overall Design: In order to increase the temporal resolution of expression profile in brain, the disease progression in those models were inverstigated in two regions of brains (cerebellum and cerebrum) at three or four time points according to the genotypes. PS-/-: new born (0d), 10 days (10d), 20 days (20d), 25 days (25d); PS-NA: new born, 4 weeks (4w), 12 weeks (12w), 18 weeks (18w); 4L/PS-NA: 4 weeks (4w), 12 weeks (12w), 18 weeks (18w). The data from those models were analyzed relative to the corresponding wild type at same time point (0d, 10d, 20d, 4w, 12w, 18w).
Chips
  • Chip ID: GSM205980 - Annotation by Bgee curators: Anatomical structure ID: MA:0000198 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205997 - Annotation by Bgee curators: Anatomical structure ID: MA:0000183 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205992 - Annotation by Bgee curators: Anatomical structure ID: MA:0000183 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205993 - Annotation by Bgee curators: Anatomical structure ID: MA:0000183 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205985 - Annotation by Bgee curators: Anatomical structure ID: MA:0000198 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205995 - Annotation by Bgee curators: Anatomical structure ID: MA:0000183 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205996 - Annotation by Bgee curators: Anatomical structure ID: MA:0000183 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205984 - Annotation by Bgee curators: Anatomical structure ID: MA:0000198 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205994 - Annotation by Bgee curators: Anatomical structure ID: MA:0000183 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205982 - Annotation by Bgee curators: Anatomical structure ID: MA:0000198 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205981 - Annotation by Bgee curators: Anatomical structure ID: MA:0000198 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM205983 - Annotation by Bgee curators: Anatomical structure ID: MA:0000198 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality

Affymetrix experiment GSE926

Experiment name Transcription profiling of murine testises collected from birth through adulthood to characterize gene expression in the testis during the progression of spermatogenesis. [GSE926]
Source GEO
Experiment description Murine testis developmental time course created from tissue samples collected from birth through adulthood and hybridized to MGU74v2 A, B, and C chips in duplicate.
Chips

Affymetrix experiment GSE9743

Experiment name Transcription profiling of mouse mutant Dstcorn1 cornea vs. wild type [GSE9743]
Source GEO
Experiment description Remodeling of the actin cytoskeleton through actin dynamics (assembly and disassembly of filamentous actin) is known to be essential for numerous basic biological processes. In addition, recent in vitro studies provided evidence that actin dynamics participate in the control of gene expression. A spontaneous mouse mutant, corneal disease 1 (corn1), is deficient for a regulator of actin dynamics, destrin (DSTN; also known as actin depolymerizing factor or ADF), and develops epithelial hyperproliferation and neovascularization in the cornea. Dstncorn1 mice exhibit the actin dynamics defect in the corneal epithelial cells as evidenced by increased filamentous actin, offering an in vivo model to investigate the physiological significance of the transcriptional regulation by actin dynamics. To examine the effect of the Dstncorn1 mutation on gene expression, we performed a microarray analysis using the cornea from Dstncorn1 and wild-type control mice. A dramatic alteration of gene expression was observed in the Dstncorn1 cornea, with 1,226 annotated genes differentially expressed. Functional annotation of these genes revealed that most significantly enriched functional categories are associated with actin and/or cytoskeleton. Among genes that belong to these categories, a considerable number of serum response factor (SRF) target genes were found, indicating the existence of the actin-SRF pathway of transcriptional regulation in vivo. A comparative study using an allelic mutant strain, Dstncorn1-2J, with milder corneal phenotypes also suggested that the severity of the actin dynamics defect correlates with the level of gene expression changes. Our study provides evidence that actin dynamics have a strong impact on gene expression in vivo. Experiment Overall Design: Microarray analysis was performed in triplicate with RNA from each genotype, A. BY H2bc H2-T18f/SnJ (A. BY wild-type), A. BY H2bc H2-T18f/SnJ-Dstncorn1/J (Dstncorn1), C57BL/6J (B6 wild-type), C57BL/6JSmn-Dstncorn1-2J/J (Dstncorn1-2J), and C.129S2(B6)-Il8rbtm1Mwm/J (Il8rb-/-), hybridized to three Affymetrix MG 430 2.0 arrays.
Chips
  • Chip ID: GSM246083 - Annotation by Bgee curators: Anatomical structure ID: MA:0000266 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM246082 - Annotation by Bgee curators: Anatomical structure ID: MA:0000266 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM246081 - Annotation by Bgee curators: Anatomical structure ID: MA:0000266 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM246072 - Annotation by Bgee curators: Anatomical structure ID: MA:0000266 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM246073 - Annotation by Bgee curators: Anatomical structure ID: MA:0000266 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
  • Chip ID: GSM246074 - Annotation by Bgee curators: Anatomical structure ID: MA:0000266 - Developmental stage ID: MmusDO:0000038
    • Probeset ID: 1435891_x_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality
    • Probeset ID: 1438786_a_at - Mapped to gene: ENSMUSG00000091474 - Detection flag: present - Quality: high quality