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Sample GSM7791666 Query DataSets for GSM7791666
Status Public on Sep 19, 2023
Title Pool3-ATAC-multiome
Sample type SRA
 
Source name tissue resident memory T cells
Organism Mus musculus
Characteristics tissue: Liver + Spleen
days p.i.: 14
replicate: 1
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated from frozen, flow cytometry sorted CD8+ T cell subsets
scATAC-seq libraries were constructed using 10X genomics reagents and protocols
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing Multiome fastq files were processed using CellRanger-ARC pipeline v2
After read alignment with bwa for ATAC, fragment files were generated by offsetting Tn5 inserts and deduplicating
After read alignment with STAR for RNA, a cell x genes count matrix was generated using the featureCounts options
Assembly: mm10
Supplementary files format and content: fragments file containing trimmed, deduplicated, high quality atac-seq fragments and cell barcodes; h5 files containing the cell x feature matrices
 
Submission date Sep 19, 2023
Last update date Sep 20, 2023
Contact name Caleb Lareau
E-mail(s) lareauc@mskcc.org
Organization name Memorial Sloan Kettering
Street address 417 E 68th St, Zuckerman - ZRC 1132
City New York
State/province New York
ZIP/Postal code 10065
Country USA
 
Platform ID GPL24247
Series (2)
GSE243593 A unique epigenomic landscape defines CD8+ tissue-resident memory T cells [multiome]
GSE243597 A unique epigenomic landscape defines CD8+ tissue-resident memory T cells
Relations
BioSample SAMN37472248
SRA SRX21828303

Supplementary file Size Download File type/resource
GSM7791666_pool3_atac_fragments.tsv.gz 133.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA

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