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| Status |
Public on Dec 07, 2021 |
| Title |
FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression [ATAC-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We used single cell Assay for Transposase-Accessible Chromatin with high-throughput sequencing (scATAC-seq) to generate chromatin accessibility profiles of mouse splenic regulatory T cells from B6 mice.
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| Overall design |
Splenic regulatory T cells (CD4+, TCRβ+, FoxP3-IRES-GFP+) and T conventional cells (CD4+, TCRβ+, FoxP3-IRES-GFP-) were sorted from 6-8 week old B6 FoxP3-IRES-GFP mice into DMEM + 2% FCS, then resuspended in PBS + 0.04% BSA. Nuclei isolation, transposition, GEM generation, and library construction targeting capture of ~12000 cells (75% Tregs, 25% Tconv) were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics). Libraries were pooled and sequenced on an Illumina NovaSeq to a final median depth of approximately 30,000 reads per cell (~80% saturation).
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| Contributor(s) |
Chowdhary K, Benoist C, Mathis D |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Dec 02, 2021 |
| Last update date |
Oct 31, 2022 |
| Contact name |
CBDM Lab |
| E-mail(s) |
cbdm@hms.harvard.edu
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| Phone |
617-432-7747
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| Organization name |
Harvard Medical School
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| Department |
Microbiology and Immunobiology
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| Lab |
CBDM
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| Street address |
77 Avenue Louis Pasteur
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE190057 |
FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression |
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| Relations |
| BioProject |
PRJNA785640 |
| SRA |
SRP348961 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190054_RAW.tar |
4.2 Gb |
(http)(custom) |
TAR (of BED, MTX, TBI, TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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