|
| Status |
Public on Jan 03, 2021 |
| Title |
SS22 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 |
SAMN13682827 |
| SRA |
SRX7442466 |
