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Series GSE66261 Query DataSets for GSE66261
Status Public on Apr 23, 2015
Title Expression and functions of long noncoding RNAs during human T helper cell differentiation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To improve our understanding of lncRNA expression in T cells, we used whole genome sequencing (RNA-seq) to identify lncRNAs expressed in human T cells and those selectively expressed in T cells differentiated under TH1, TH2, or TH17 polarizing conditions. The majority of these lineage-specific lncRNAs are co-expressed with lineage-specific protein-coding genes. These lncRNAs are predominantly intragenic with co-expressed protein-coding genes and are transcribed in sense and antisense orientations with approximately equal frequencies. Further, genes encoding TH lineage specific mRNAs are not randomly distributed across the genome but are highly enriched in the genome in genomic regions also containing genes encoding TH lineage-specific lncRNAs. Our analyses also identify a cluster of antisense lncRNAs transcribed from the RAD50 locus that are selectively expressed under TH2 polarizing conditions and co-expressed with IL4, IL5 and IL13 genes. Depletion of these lncRNAs via selective siRNA treatment demonstrates the critical requirement of these lncRNAs for expression of the TH2 cytokines, IL-4, IL-5 and IL-13. Collectively, our analyses identify new lncRNAs expressed in a TH lineage specific manner and identify a critical role for a cluster of lncRNAs for expression of genes encoding TH2 cytokines.
Overall design Human peripheral blood mononuclear cells (PBMC) were cultured under TH1, TH2, and TH17 polarizing conditions. TH1, TH2, and TH17 primary and effector cultures were isolated and poly(A)+ and total RNA sequencing performed.
Contributor(s) Spurlock III CF, Tossberg JT, Guo Y, Collier SP, Crooke III PS, Aune TM
Citation(s) 25903499
Submission date Feb 24, 2015
Last update date May 15, 2019
Contact name Charles F Spurlock III
Phone 6153432363
Organization name Vanderbilt University School of Medicine
Department Medicine
Lab T3113
Street address 1161 21st Avenue South
City Nashville
State/province Tennessee
ZIP/Postal code 37232
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM1618311 TH1 Primary_2695
GSM1618312 TH2 Primary_2695
GSM1618313 TH17 Primary_2695
BioProject PRJNA276277
SRA SRP055474

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Supplementary file Size Download File type/resource
GSE66261_read_count_table.txt.gz 912.1 Kb (ftp)(http) TXT
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