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Series GSE75111 Query DataSets for GSE75111
Status Public on Nov 20, 2015
Title Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [TGFB1_IL6-48h-IL-17A/GFP+]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Extensive cellular heterogeneity exists within specific immune-cell subtypes classified as a single lineage, but its molecular underpinnings are rarely characterized at a genomic scale. Here, we use single-cell RNA-seq to investigate the molecular mechanisms governing heterogeneity and pathogenicity of Th17 cells isolated from the central nervous system (CNS) and lymph nodes (LN) at the peak of autoimmune encephalomyelitis (EAE) or polarized in vitro under either pathogenic or non-pathogenic differentiation conditions. Computational analysis reveals a spectrum of cellular states in vivo, including a self-renewal state, Th1-like effector/memory states and a dysfunctional/senescent state. Relating these states to in vitro differentiated Th17 cells, unveils genes governing pathogenicity and disease susceptibility. Using knockout mice, we validate four novel genes: Gpr65, Plzp, Toso and Cd5l (in a companion paper). Cellular heterogeneity thus informs Th17 function in autoimmunity, and can identify targets for selective suppression of pathogenic Th17 cells while sparing non-pathogenic tissue-protective ones.
 
Overall design Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h
 
Contributor(s) Gaublomme J, Yosef N, Regev A
Citation(s) 26607794, 31197158
Submission date Nov 17, 2015
Last update date Jul 02, 2019
Contact name Nir Yosef
E-mail(s) niryosef@berkeley.edu
Phone (617) 714-7734
Organization name UC Berkeley
Department EECS
Lab Yosef
Street address Berkeley
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
Samples (151)
GSM1943374 Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC14_56
GSM1943375 Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC16_56
GSM1943376 Tgfb1_IL6-IL17A_POS_48hr_130118_T16_48h_SC19_56
This SubSeries is part of SuperSeries:
GSE74833 Identification of novel regulators of Th17 cell pathogenicity by single-cell genomics
Relations
BioProject PRJNA302457
SRA SRP066322

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75111_RAW.tar 132.5 Mb (http)(custom) TAR (of FPKM_TRACKING)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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