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Series GSE148981 Query DataSets for GSE148981
Status Public on Nov 25, 2020
Title An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary This SuperSeries is composed of the SubSeries listed below.

ab lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I or MHC II-presented antigens, are essential for immune responses and develop from CD4+CD8+ thymocytes. The absence of in vitro models and the heterogeneity of ab thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA and ATAC (chromatin accessibility) sequencing, we identified mouse and human ab thymocyte developmental trajectories. We demonstrated asymmetric emergence of CD4+ and CD8+ lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. Through computational analysis of single-cell data and binding sites for the CD4+ lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4+ or CD8+ lineage differentiation, and with expression of Thpok or of the CD8+ lineage factor Runx3. Our findings provide insight into the mechanisms of CD4+ and CD8+ T cell differentiation and a foundation for mechanistic investigations of ab T cell development.
 
Overall design Refer to individual Series
 
Citation(s) 33242395
Submission date Apr 20, 2020
Last update date Jan 05, 2021
Contact name Remy Bosselut
E-mail(s) bosselur@helix.nih.gov
Phone 240-760-6866
Organization name National Cancer Institute, National Institute of Health
Department Laboratory of Immune Cell Biology
Lab Bosselut
Street address 9000 Rockville Pike, Building 37
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (5)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (78)
GSM4486831 Chopp1: Unsignaled DP thymocytes replicate 1
GSM4486832 Chopp2: Unsignaled DP thymocytes replicate 2
GSM4486833 Chopp3: Unsignaled DP thymocytes replicate 3
This SuperSeries is composed of the following SubSeries:
GSE148973 An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (RNAseq EXP1)
GSE148974 An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (RNAseq Exp2)
GSE148975 An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Population ATACseq)
Relations
BioProject PRJNA626648

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Supplementary file Size Download File type/resource
GSE148981_RAW.tar 13.5 Gb (http)(custom) TAR (of BW, CSV, H5, TAB, TBI, TSV, TXT)
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