|
| Status |
Public on Jul 22, 2023 |
| Title |
SOCS1-KO-1 |
| Sample type |
SRA |
| |
|
| Source name |
AT-3
|
| Organism |
Mus musculus |
| Characteristics |
cell line: AT-3
cell type: Breast Cancer
genotype: SOCS1-KO
treatment: stimulation with IFNgamma and TNF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Gene edited AT-3 breast cancer cells 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 mm10 genome with bowtie2
Peaks were called with Macs2
Assembly: mm10
Supplementary files format and content: Peak files called with macs2
|
| |
|
| Submission date |
Jul 21, 2023 |
| Last update date |
Jul 22, 2023 |
| 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 |
GPL19057 |
| Series (2) |
| GSE237967 |
A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity (AT3 ATAC-Seq) |
| GSE237974 |
A novel CRISPR/Cas9 screening platform identifies an IRF1-SOCS1-mediated negative feedback loop that limits CXCL9 expression and anti-tumor immunity |
|
| Relations |
| BioSample |
SAMN36679480 |
| SRA |
SRX21126600 |
