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Sample GSM4232772 Query DataSets for GSM4232772
Status Public on Jan 03, 2021
Title SS18 ATAC-seq
Sample type SRA
 
Source name Peripheral blood CD8+ T cells
Organism Homo sapiens
Characteristics response: Progressive disease
tissue: Peripheral blood
cell type: Primary CD8+ T cells
disease state: gastric cancer
Growth protocol To obtain CD8+ T cells from thawed PBMCs were stained with appropriate antibodies (Abs), and sorted into CD8+ T cells using a BD FACSAria III™ cell sorter (BD Biosciences, San Jose, CA, USA).
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated from CD8+ T cells and subjected to the transposition reaction with Illumina transposase in 1× Tagment DNA (TD) buffer
Library fragments were amplified with indexing primers from Nextera kit (Illumina, San Diego, CA, USA)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Basecalls performed using CASAVA version 1.8.2.
ATAC-seq reads were processed using Trimmomatic software.
ATAC-seq reads were aligned to the hg19 genome assembly using bowtie2 v2.3.4.1 with "-k 4 -N 1 -R 5 --end-to-end" options.
The aligned reads were converted into browser extensible data (BED) format using “bedtools bamtobed”, and offset +4 base pair (bp) for positive strand and −5 bp for negative strand.
The aligned reads were used for peak calling process using HOMER suite with “findPeaks” with “-style factor -tbp 3 -region” option.
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs (BWs), genome-wide ATAC-seq signal enrichment.
 
Submission date Dec 26, 2019
Last update date Jan 03, 2021
Contact name Hyun Mu Shin
E-mail(s) hyunmu.shin@snu.ac.kr
Organization name Seoul National University College of Medicine
Department Biomedical Sciences
Lab Laboratory of Immunobiology
Street address Biomedical Science Building 202, 103 Daehakro, Jongro-gu
City Seoul
ZIP/Postal code 110-799
Country South Korea
 
Platform ID GPL18573
Series (1)
GSE142604 The chromatin accessibility of circulating CD8+ T cells predicts immune-therapeutic response of PD-1 blockade in gastric cancer
Relations
BioSample SAMN13682832
SRA SRX7442462

Supplementary file Size Download File type/resource
GSM4232772_SS17.bw 728.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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