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| Status |
Public on Sep 02, 2022 |
| Title |
ATAC_DN67_AAVS1_unstim |
| Sample type |
SRA |
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| Source name |
primary T cells
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| Organism |
Homo sapiens |
| Characteristics |
treatment: unstimulated
genotype: AAVS1-null
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| Treatment protocol |
cells were stimulated with anti-idiotye antibody for 3 hours
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| 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
Genome_build: hg38
Supplementary_files_format_and_content: bigwig genome wide signal track
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| Submission date |
May 11, 2021 |
| Last update date |
Sep 03, 2022 |
| Contact name |
Julia Belk |
| Organization name |
Stanford University
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| Street address |
450 Serra Mall
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN19110078 |
| SRA |
SRX10853023 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5290975_atac_DN67_AAVS1_unstim-coverage-depth-norm.bw |
123.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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