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E-GEOD-58435 - Amniotic fluid RNA gene expression profiling provides insights into the phenotype of Turner syndrome

Status
Released on 13 June 2014, last updated on 21 June 2014
Organism
Homo sapiens
Samples (10)
Array (1)
Protocols (5)
Description
Background: Turner syndrome, a common sex chromosome aneuploidy, has characteristics and malformations associated with the phenotype. Fetal amniotic fluid is a complex biological material that could contribute to the understanding Turner syndrome pathogenesis. Global gene expression analysis of Turner syndrome fetal amniotic fluid supernatant was utilized to identify organ systems and specific genes that may play a role in the pathophysiologic changes that are seen in individuals with Turner syndrome. Methods: Global gene expression analysis was performed utilizing cell-free RNA from five midtrimester fetuses with Turner syndrome matched with five euploid female fetuses. Total RNA was extracted, amplified, hybridized onto GeneChip® Human Genome U133 Plus 2.0 arrays. Network and pathway analysis of differentially expressed genes were completed. Chromosomal distribution of gene expression differences, differential expression by pathway and organ system (a “Turner syndrome core transcriptome”), and candidate genes that could play a pathological role were identified. Results: There were 470 differentially expressed genes identified in the Turner syndrome transcriptome. The differentially expressed genes were distributed randomly across different chromosomes. Among genes on the X chromosome, XIST was down-regulated, and SHOX not differentially expressed. The most highly represented organ systems were hematologic/immune and neurologic. Increased representation of differentially expressed genes in the hematologic/immune system distinguishes the Turner syndrome transcriptome from the euploid, trisomy 18 and trisomy 21 transcriptomes previously studied in our laboratory. Manual curation of the differentially expressed gene list identified genes including NFATC3, IGFBP5, and LDLR that warrant further study. 2nd trimester amniotic fluid mRNA expression was compared between 5 Turners and 5 euploid fetuses.
Experiment type
transcription profiling by array 
Contacts
Heather C Wick <hwick@cs.tufts.edu>, Diana W Bianchi, Donna K Slonim, Kirby L Johnson, Lauren J Massingham, Thomas Scholl
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-58435.idf.txt
Sample and data relationshipE-GEOD-58435.sdrf.txt
Raw data (1)E-GEOD-58435.raw.1.zip
Processed data (1)E-GEOD-58435.processed.1.zip
Array designA-AFFY-44.adf.txt
Links