 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 09, 2022 |
| Title |
ATAC_DN12_CD4_MED12 |
| Sample type |
SRA |
| |
|
| Source name |
primary T cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: unstimulated
genotype: MED12-null
chip antibody: none
|
| Treatment protocol |
cells were stimulated with anti-idiotype antibody for 3 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATACseq: Approximately 100k CAR-T cells were used from each sample. Nuclei were isolated with ATAC-LB (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) . ChIP: CAR-T cells (3 x 106) were double crosslinked by 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30 minutes followed by 10 minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level – 10, Duty Cycle – 5, PIP – 140, Cycles/Burst – 200, Time – 4 minutes). Sheared chromatin was immunoprecipitated overnight.
ATACseq libraries were prepared with Nextera DNA Library Preparation Kit (Illumina). ChIPseq libraries were prepared with Ovation Ultralow Library System V2 (Tecan).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
reads were trimmed with fastp
reads were aligned to hg38 with hisat2
reads were deduplicated using picard
peaks were called using macs2
normalized bigwig files were generated using Rtracklayer
Assembly: hg38
Supplementary files format and content: bigwig genome wide signal track
|
| |
|
| Submission date |
Sep 09, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Julia Belk |
| Organization name |
Stanford University
|
| Street address |
450 Serra Mall
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE174281 |
Genome-wide maps of chromatin state in human primary CAR-T cells [ChIPseq, ATAC-seq] |
| GSE174282 |
Genome-wide maps of chromatin state in human primary CAR-T cells |
|
| Relations |
| BioSample |
SAMN30755065 |
| SRA |
SRX17504598 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6568615_ATAC_DN12_CD4_MED12-coverage-tss-norm.bw |
147.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
