|
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 |