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| Status |
Public on Nov 25, 2020 |
| Title |
An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Thpok ChIPSeq) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
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.
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| Overall design |
Streptavidin immunoprecipitation from the chromatin of CD4+ SP cells isolated from thymi of ThpokBio/+ Rosa26BirA or Rosa26BirA animals
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| |
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| Contributor(s) |
Chopp LB, Bosselut R |
| Citation(s) |
33242395 |
| |
| Submission date |
Apr 20, 2020 |
| Last update date |
Jan 05, 2021 |
| Contact name |
Remy Bosselut |
| E-mail(s) |
[email protected]
|
| 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 |
| |
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| Platforms (1) |
|
| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE148981 |
An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development |
|
| Relations |
| BioProject |
PRJNA626652 |
| SRA |
SRP257567 |
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