|
| Status |
Public on Dec 23, 2022 |
| Title |
CD4_activation_ATAC-seq_B1T1 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: TCR activated CD4+ T cells
cell numbers: 50,000
|
| Treatment protocol |
TCR activation: The isolated primary CD4+ T cells were cultured in RPMI medium supplemented with 10% FBS/penicillin-streptomycin at 37 °C incubator and activated by 2 ug/ml of plate-bound anti-CD3 and 1 ug/ml of suspended anti-CD28 for 72 hours. IL-2 stimulation: The above TCR-activated T cells were rested overnight. Two hundred International Units of IL-2 were added to the cells for 4 hours.
|
| Growth protocol |
Resting CD4+ T cell isolation: A buffycoat was obtained from Blood Bank in National Institute of Health. Human CD4+ T cells were purified by EasySep Human CD4+ T cell isolation kit (StemCell Technology; 17952).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
not provided
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw paired-end reads were quality trimmed using Trim Galore version 0.6.6 (options: --stringency 3 -q 30 -e .20 --length 16) and mapped to the hg38 genome using BWA 0.7.17 (command: mem). The duplicate reads were removed from the alignment file and MACS v2.2.7.1 callpeak command was used to generate bedgraph (options: --nomodel --extsize 150 --shift -75 -B --SPMR) which then converted to bigwig format.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq coverage; bigwig format.
|
| |
|
| Submission date |
Jan 19, 2022 |
| Last update date |
Dec 23, 2022 |
| Contact name |
Chia-Lin Wei |
| Organization name |
The Jackson Laboratory
|
| Department |
Genome Technologies
|
| Street address |
10 Discovery Dr
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE194036 |
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs |
|
| Relations |
| BioSample |
SAMN25125411 |
| SRA |
SRX13834321 |
