E-GEOD-43005 - Profiling of human CD4+ T subsets identifies a Th2-specific non-coding RNA GATA3-AS1

Status
Released on 1 June 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (24)
Array (1)
Protocols (5)
Description
Host defense against diverse pathogens involves the recruitment and differentiation of CD4+ T effector subsets including T helper 1 (Th1), Th2, Th17 and induced regulatory T (Treg) cells. Surface phenotype studies have revealed subset-specific surface markers for the identification and purification of human primary CD4+ T effector subsets. In the present study, we aimed to characterize the mRNA and large intergenic non-coding RNA (lincRNA) expression differences between human primary CD4+ T effector subsets and identify potential subset-specific genes. To achieve this goal, mRNA and lincRNA microarray profiling of flow cytometry-sorted human primary Th1, Th2, Th17 and Treg cells was performed. Principal component and pathway analyses revealed subset-specific gene expression patterns. A Th2-specific lincRNA, GATA3-AS1, also termed FLJ45983, was identified in primary immune cells and tissues, as well as in in vitro polarized CD4+ T effector subsets. Further analysis showed that GATA3-AS1 was a potential diagnostic marker in allergy, a Th2-associated disease. This first systematic genome-wide analysis of gene expression differences between primary CD4+ T effector subsets may help to identify novel regulatory protein-coding genes and lincRNAs regulating CD4+ T cell subset differentiation, as well as potential diagnostic markers. As an example, we identified a GATA3-associated Th2-specific marker lincRNA GATA3-AS1. Gene expression microarray analysis of flow-cytometry sorted human primary naïve CD4+ T cells, CD4+ T central memory cells, Th1, Th2, Th17 and Treg cells from buffy coat of four healthy controls Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8X60K microarray.
Experiment type
transcription profiling by array 
Contacts
Hui Wang <hui.wang@gu.se>, Colm Nestor, Huan Zhang, Mikael Benson, Shuli Zhao
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-43005.idf.txt
Sample and data relationshipE-GEOD-43005.sdrf.txt
Raw data (1)E-GEOD-43005.raw.1.zip
Processed data (1)E-GEOD-43005.processed.1.zip
Array designA-GEOD-16083.adf.txt
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