Bgee: Gene Expression Evolution

Expression data retrieved for the gene ENSG00000156398: SFXN2 - in the anatomical structure: "unknown" at the stage: "Human developmental stage" - Homo sapiens

Query parameters Anatomical structure: unknown
Stage: Human developmental stage
Gene: ENSG00000156398 - SFXN2
Data parameters
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Affymetrix experiment GSE13433

Experiment name Transcription profiling of human alveolar soft-part sarcoma (ASPS) [GSE13433]
Source GEO
Experiment description Alveolar soft-part sarcoma (ASPS) is an extremely rare, highly vascular soft tissue sarcoma affecting predominantly adolescents and young adults. In an attempt to gain insight into the pathobiology of this enigmatic tumor, we performed the first genome-wide gene expression profiling study. Experiment Overall Design: For seven patients with confirmed primary or metastatic ASPS, RNA samples were isolated immediately following surgery, reverse transcribed to cDNA and each sample hybridized to duplicate high-density human U133 plus 2.0 microarrays. Array data was then analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome. Subsequent gene ontology analysis was used to identify transcripts with therapeutic or diagnostic potential. A subset of the most interesting genes was then validated using quantitative RT-PCR and immunohistochemistry.

Affymetrix experiment GSE23906

Experiment name Evaluation of gene expression data generated from expired Affymetrix GeneChip__ microarrays using MAQC reference RNA samples [GSE23906]
Source GEO
Experiment description The Affymetrix GeneChipR system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip____ microarrays unprocessed before their manufacturer's expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer's expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80 C, were stable over a time frame of at least four years. The new gene expression data were generated with 12 microarrays (2 types of microarrays x 2 samples x 3 replicates). Three replicates for each of the two MAQC samples (A = Stratagene's Universal Human Reference RNA; B = Ambion's Human Brain Reference RNA) were profiled in 2009 by using both the expired U133A microarrays (expired in 2004) and the unexpired U133Plus2 microarrays. In addition, gene expression data generated with unexpired U133Plus2 microarrays (AFX), other microarray platforms, and TaqManR assays by the MAQC project in 2005 were used as references to assess the stability of the MAQC samples stored at -80 C for four years by comparing new microarray data with those obtained four years ago. The MAQC reference data also allowed for further evaluation of the usefulness of the data generated with expired U133A microarrays.

Affymetrix experiment GSE3061

Experiment name Transcription profiling of human Stratagene Universal RNA on Affymetrix U133 Plus 2.0 and U133 A Chips [GSE3061]
Source GEO
Experiment description Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Experiment Overall Design: Stratagene universal human RNA was processed using 5 aliquots of 2 ug each. The samples were hybridized to both 133 Plus 2.0 and 133 A arrays.