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Status |
Public on Dec 07, 2021 |
Title |
scATAC.Treg.Tconv |
Sample type |
SRA |
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Source name |
Treg.Tconv
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: spleen genotype: wt
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Extracted molecule |
genomic DNA |
Extraction protocol |
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, and GEM generation 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). 0.1x lysis buffer was used for cell lysis and nuclei isolation. Library construction was carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Fastq files were generated from BCL files using bcl2fastq. Fastq files were aligned to the mm10 genome and used to create count matrices using the cellRanger ATAC pipeline using cellranger-atac count (v1.2, 10x Genomics) Fragments were intersected with open chromatin regions previously defined by the ImmGen consortium (Yoshida et al, Cell, 2019) to create an intial OCR x cell counts matrix. Preprocessing was done using Signac (v1.1), retaining cells with at least 4000 fragments per cell, greater than 55 percent reads in peaks, TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05. Putative doublets were removed using Archr (v0.9.3) Archr (v0.9.3) was used to call cluster-specific peaks using MACS2. To create a final peak set, MACS2 peak calls were compared with OCRs defined by the ImmGen consortium in Yoshida et al. In cases where MACS2 peak calls overlapped ImmGen OCRs, the Immgen reference peak was kept. Any MACS2 peaks not overlapping OCRs in the ImmGen dataset were added to this list to create a final merged Treg-specific peak set. Immgen peaks without overlapping MACS2 calls from this dataset were not included in the final Treg peak set. Genome_build: mm10 Supplementary_files_format_and_content: .mtx counts matrix; .tsv cell barcodes list; .tsv OCR locations; .fragments.tsv.gz fragments file; .fragments.tsv.gz.tbi fragments index file
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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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Platform ID |
GPL24247 |
Series (2) |
GSE190054 |
FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression [ATAC-seq] |
GSE190057 |
FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression |
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Relations |
BioSample |
SAMN23572792 |
SRA |
SRX13289171 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5712663_Spleen_Treg_Metadata.txt.gz |
139.5 Kb |
(ftp)(http) |
TXT |
GSM5712663_Spleen_Treg_Tconv_Metadata.txt.gz |
178.1 Kb |
(ftp)(http) |
TXT |
GSM5712663_Spleen_Treg_Tconv_barcodes.tsv.gz |
28.7 Kb |
(ftp)(http) |
TSV |
GSM5712663_Spleen_Treg_barcodes.tsv.gz |
22.7 Kb |
(ftp)(http) |
TSV |
GSM5712663_barcodes.tsv.gz |
28.7 Kb |
(ftp)(http) |
TSV |
GSM5712663_celltype_metadata.txt.gz |
32.2 Kb |
(ftp)(http) |
TXT |
GSM5712663_counts.mtx.gz |
375.9 Mb |
(ftp)(http) |
MTX |
GSM5712663_fragments.tsv.gz |
3.9 Gb |
(ftp)(http) |
TSV |
GSM5712663_fragments.tsv.gz.tbi.gz |
1.2 Mb |
(ftp)(http) |
TBI |
GSM5712663_peaks.bed.gz |
2.3 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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