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Series GSE75108 Query DataSets for GSE75108
Status Public on Nov 20, 2015
Title Single-cell transcriptional profiling of Th17 cells, harvested at peak of disease in EAE from LN [EAE-LN-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, harvested at peak of disease in EAE from LN
 
Contributor(s) Gaublomme J, 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 (136)
GSM1942969 EAE-IL17A-LN_1_AAGAGGCA_ACTGCATA_181
GSM1942970 EAE-IL17A-LN_1_AAGAGGCA_AGAGTAGA_181
GSM1942971 EAE-IL17A-LN_1_AAGAGGCA_GTAAGGAG_181
This SubSeries is part of SuperSeries:
GSE74833 Identification of novel regulators of Th17 cell pathogenicity by single-cell genomics
Relations
BioProject PRJNA302460
SRA SRP066317

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
GSE75108_RAW.tar 115.6 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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