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Series GSE103968 Query DataSets for GSE103968
Status Public on Jul 23, 2018
Title Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [ATAC-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary T cell development and selection is orchestrated in the thymus by a specialized niche of diverse stromal populations. By transcriptional single cell sorting, we de novo characterize the entire stromal compartment of the thymus. We identified dozens of cell states within the thymic stroma, with thymic epithelial cells (TEC) showing the highest degree of heterogeneity. Our analysis highlights four major medullary TEC (mTEC I-IV) populations, with distinct molecular functions, epigenetic landscapes and lineage regulators. Specifically, mTEC-IV constitutes a new and highly divergent TEC lineage with molecular characteristics of the gut chemosensory epithelial tuft cells. Mice deficient of Pou2f3, a tuft cells master regulator, resulted in complete and specific depletion of mTEC-IV, without affecting other TEC populations. Overall, our study comprehensively defines all stroma cells in the thymus and identifies a new TEC lineage associated with chemosensory properties that may potentially link the adaptive immune system to environmental and neurological signals.
 
Overall design Transcriptional profiling of single cells from the stroma of mouse thymus, generated from deep sequencing of tens of thousands of cells, reveled 4 subpopulations of medullary epithelial cells. ATAC-seq assay profile the accessible chromatin landscape of these subpopulation.
 
Contributor(s) Amit I, Abramson J, Bornstein C, Nevo S, Giladi A, Kadouri N
Citation(s) 30022162
Submission date Sep 18, 2017
Last update date May 15, 2019
Contact name Ido Amit
E-mail(s) ido.amit@weizmann.ac.il
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (8)
GSM2787108 mTEC-I_rep1_ATAC
GSM2787109 mTEC-I_rep2_ATAC
GSM2787110 mTEC-II_rep1_ATAC
This SubSeries is part of SuperSeries:
GSE103970 Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage
Relations
BioProject PRJNA407805
SRA SRP117952

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
GSE103968_ATAC-TEC_merged_annotated_peaks_counts.txt.gz 7.7 Mb (ftp)(http) TXT
GSE103968_RAW.tar 4.7 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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