|
| Status |
Public on Jan 18, 2024 |
| Title |
Stim_FOXO1_CD8 rep3 (ATAC-seq) |
| Sample type |
SRA |
| |
|
| Source name |
PMBC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PMBC
cell type: T cell
genotype: FOXO1 overexpressing
treatment: Stimulated 16 hours with MCF7 tumors
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD8+ CAR T cells were harvested at a concentration of 500,000 cells/ml. 50,000 cells were lysed using the ZYMO research DNA isolation kit. Tagmentation then purification was performed on DNA, and isolated chromatin was amplified.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Reads were trimmed for adaptor sequence using Ngmerge, then mapped to the hg38 genome with bowtie2
Peaks were called with Genrich
Assembly: GRCh38
Supplementary files format and content: Peak files called with Genrich
|
| |
|
| Submission date |
Feb 17, 2023 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Kevin C sek |
| E-mail(s) |
kevin.sek@petermac.org
|
| Phone |
0432960331
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Cancer Immunology
|
| Lab |
Beavis Lab
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE225521 |
Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors [Human ATACseq CD8] |
| GSE225527 |
Overexpression of FOXO1 enhances CAR T cell polyfunctionality, metabolic fitness and efficacy against solid tumors |
|
| Relations |
| BioSample |
SAMN33337714 |
| SRA |
SRX19401315 |
