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Sample GSM5712663 Query DataSets for GSM5712663
Status Public on Dec 07, 2021
Title scATAC.Treg.Tconv
Sample type SRA
 
Source name Treg.Tconv
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: spleen
genotype: wt
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).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Dec 02, 2021
Last update date Oct 31, 2022
Contact name CBDM Lab
E-mail(s) cbdm@hms.harvard.edu
Phone 617-432-7747
Organization name Harvard Medical School
Department Microbiology and Immunobiology
Lab CBDM
Street address 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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