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Series GSE121080 Query DataSets for GSE121080
Status Public on Oct 08, 2019
Title Single cell RNA-seq resolves lineage-specific activation dynamics of human blood and tissue T cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Human T cells coordinate adaptive immunity and persist as heterogeneous subsets in tissues and circulation, yet the impact of localization on T cell function remains unclear. Here, we profile activation of T cells from human lungs, lymph nodes (LN), bone marrow (BM) and blood following TCR/CD3 stimulation by single cell RNA-seq. Analysis of >50,000 individual resting and activated T cells using new factorization methods reveals conserved lineage-specific gene expression signatures and activation trajectories across sites. CD4 T cells exhibit a transient intermediate activation state while CD8 T cells show an “all-off/all-on” activation pattern. Lung and LN T cells exhibit tissue-specific profiles, while blood T cells closely resemble those in BM. Our results define the lineage-specific activation dynamics of human T cells from different anatomical sites.
 
Overall design Here, we profile activation of T cells from human lungs, lymph nodes (LN), bone marrow (BM) and blood following TCR/CD3 stimulation by single cell RNA-seq.
 
Contributor(s) Szabo P, Mendes Levitin H, Farber DL, Sims PA
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Submission date Oct 10, 2018
Last update date Oct 09, 2019
Contact name Peter A Sims
E-mail(s) pas2182@columbia.edu
Organization name Columbia University
Street address 3960 Broadway, Lasker 203AC
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (16)
GSM3425686 Donor 1 resting lung
GSM3425687 Donor 1 activated lung
GSM3425688 Donor 1 resting bone marrow
Relations
BioProject PRJNA495590
SRA SRP164917

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
GSE121080_RAW.tar 114.0 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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