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| Status |
Public on Oct 25, 2020 |
| Title |
scRNA-seq of mouse thymocyte CD4 CD8 lineage choice and differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
CD4 and CD8 identify helper and cytotoxic T cell lineages, and serve as co-receptors for MHC-restricted TCR recognition. Despite decades of investigation, questions remain about how TCR specificity and co-receptor gene expression are matched during T cell repertoire selection. Here we address the order and logic of CD4/CD8 lineage choice and differentiation by scRNA-seq. Maturation, activation, and lineage specification emerged as principle components, in this order. Co-receptor gene expression uncovered waves of Cd4+Cd8a+, Cd4+Cd8a- and Cd4-Cd8a+ selection intermediates and revealed gene expression programs associated with each pattern, including TCR- and cytokine signaling genes, lineage markers and transcription factors. While in the unperturbed thymus early Cd4+Cd8a+ selection intermediates were followed first by CD4-like Cd4+Cd8a- and later by CD8-like Cd4-Cd8a+ selection intermediates, the order of co-receptor gene expression was not inherently fixed. These data provide a benchmark for models of CD4/CD8 lineage choice, and a rich resource for interrogating T cell differentiation.
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| Overall design |
Thymocyte cell suspensions from two wild type C57BL/6 thymi and one MHC class II-deficient thymus (Madsen et al., Proc Natl Acad Sci U S A. 1999; 96: 10338-43) were stained with antibodies to CD4, CD8a, TCRb and CD69-. Single cells representing thymocytes before, during and after lineage choice and differentiation (CD4+ CD8+ Cd69, CD4+ CD8+ Cd69+, CD4+ CD8+ TCRbhi , CD4+ CD8low, CD4+ CD8 -, and CD4- CD8+ TCRbhi) were sorted by flow cytometry into 96 well plates containing lysis buffer for construction of RNA-seq libraries.
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| Contributor(s) |
Karimi MM, Pallikonda HA, Heyn H, Merkenschlager M |
| Citation(s) |
33397934 |
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| Submission date |
Apr 23, 2020 |
| Last update date |
Jan 19, 2021 |
| Contact name |
LMS Bioinformatics Core |
| E-mail(s) |
bioinformatics@lms.mrc.ac.uk
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| Organization name |
MRC London Institute of Medical Sciences
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| Department |
Bioinformatics Core
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| Street address |
Hammersmith Hospital Campus, Du Cane Road
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| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (1495)
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| Relations |
| BioProject |
PRJNA627664 |
| SRA |
SRP258118 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149207_Read_Counts_Matrix_All_Samples.csv.gz |
8.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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