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Series GSE122740 Query DataSets for GSE122740
Status Public on Nov 20, 2019
Title Single cell RNA sequencing identifies the developmental origin of C-Myc dependent T-bet+thymic intraepithelial lymphocyte precursor
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Natural intraepithelial lymphocytes (IELs) are thymus-derived adaptive immune cells, which are important contributors to intestinal immune homeostasis. Similar to other innate-like T cells they are induced in the thymus through high-avidity interaction that would otherwise lead to clonal deletion in conventional CD4 and CD8 T cells. By applying single-cell RNA-sequencing (scRNA-seq) on a heterogeneous population of IEL precursors (IELPs) we define a developmental trajectory that identifies Id3 as a novel regulator of IELP development and shows that all natural TCRαβ+ IELPs progress through a PD-1 stage as a result of strong agonist selection. Furthermore, with the use of newly developed PD-1 fate map and conditional T-bet knockout mice we demonstrate that this PD-1 stage precedes the induction of T-bet. The transition from PD-1 to T-bet is regulated by the transcription factor C-Myc, as T cell-specific conditional C-myc knockout mice lack PD-1-T-bet+ IELPs, while PD-1+T-bet- IELPs are still present. In summary, our results provide a high-resolution molecular framework for thymic IEL development and deepen our understanding of this still elusive cell type.
Overall design Single cell RNA sequencing was performed on thymic intraepithelial lymphocytes by sorting CD4-CD8-TCRb+NK1.1+ fresh isolated thymocytes from one TBGR mouse. A replicating experiment was executed by comparing fresh isolated IELPs from one TBGR and TGBR C-mycD/DCd4 mouse.
Please note that some of the readme_*.coutt.txt files are identical, because the same cell barcodes have been used but different illumina barcodes.
Contributor(s) Hummel J, Zeis P, Grün D, Tanriver Y
Citation(s) 31712600
Submission date Nov 20, 2018
Last update date Nov 20, 2019
Contact name Patrice Zeis
Organization name Max Planck Institute of Immunobiology and Epigenetics
Lab Dominic Grün
Street address Stübeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (20)
GSM3484427 IEL_15_1
GSM3484428 IEL_15_2
GSM3484429 IEL_16_1
BioProject PRJNA506214
SRA SRP169866

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE122740_RAW.tar 6.9 Mb (http)(custom) TAR (of CSV, TXT)
GSE122740_celseq_barcodes.192.txt.gz 910 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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