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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 20, 2015 |
| Title |
Population transcriptional profiling of Th17 cells, isolated from CNS or LN at peak of disease in EAE |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| Overall design |
Population transcriptional profiling of Th17 cells, isolated from CNS or LN at peak of disease in EAE
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| Contributor(s) |
Gaublomme J, Yosef N, Regev A |
| Citation(s) |
26607794, 31197158 |
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| Submission date |
Nov 17, 2015 |
| Last update date |
Jul 02, 2019 |
| Contact name |
Nir Yosef |
| E-mail(s) |
[email protected]
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| Phone |
(617) 714-7734
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| Organization name |
UC Berkeley
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| Department |
EECS
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| Lab |
Yosef
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| Street address |
Berkeley
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE74833 |
Identification of novel regulators of Th17 cell pathogenicity by single-cell genomics |
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| Relations |
| BioProject |
PRJNA302463 |
| SRA |
SRP066312 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE75105_RAW.tar |
5.8 Mb |
(http)(custom) |
TAR (of FPKM_TRACKING) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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