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Series GSE122846 Query DataSets for GSE122846
Status Public on Nov 24, 2018
Title Single cell profiling of CD4+ T cells from human fetal intestine
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T-cells reside in the fetal intestine. We combined functional assays with mass cytometry, single-cell RNA-sequencing, and high-throughput TCR-sequencing to characterize the fetal intestinal CD4+ T-cell compartment. We identified 22 CD4+ T-cell clusters, including naive-like, regulatory-like, and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like cells expressed high levels of Ki-67, indicating cell division, and CD5, a surrogate marker of TCR-avidity, and produced IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR-repertoire analysis demonstrated clonal expansions, distinct repertoire characteristics, and interconnections between subpopulations of memory-like CD4+ T-cells. Imaging-mass cytometry further showed that memory-like CD4+ T-cells colocalized with antigen-presenting cells. Collectively, these results provided evidence for the generation of memory-like CD4+ T-cells in the human fetal intestine, consistent with exposure to foreign antigens.
 
Overall design Single, live, CD3+CD8a–TCRγδ–CD4+/– T-cells from one human fetal intestines were processed on the Chromium 3' single cell platform (10x Genomics) and sequenced on an Illumina HiSeq 4000.
 
Contributor(s) Li N, Koning F, Kloet SL
Citation(s) 30664737
Submission date Nov 23, 2018
Last update date Mar 21, 2019
Contact name Na Li
E-mail l.li@lumc.nl
Phone +31715261820
Organization name LUMC
Street address Albinusdreef 2
City Leiden
ZIP/Postal code 2333 ZA
Country Netherlands
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (1)
GSM3486911 CD4+ T cells #6
Relations
BioProject PRJNA506660
SRA SRP170417

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
GSE122846_RAW.tar 13.1 Mb (http)(custom) TAR (of H5, MTX, TSV)
Raw data are available in SRA
Processed data provided as supplementary file

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