|
| Status |
Public on Feb 05, 2024 |
| Title |
R1192C_MUT, replicate 3, bulkATAC |
| Sample type |
SRA |
| |
|
| Source name |
CA46
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CA46
genotype: Smarca4 R1192C/+
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014, Zymo Research)
ATAC-seq libraries were generated following the Omni-ATAC protocol. Libraries were barcoded and amplified with KAPA HiFi HotStart ReadyMix (KK2602, Roche). Library size distribution and concentration was evaluated using the Agilent 4200 TapeStation system and Qubit dsDNA HS Assay Kit (ThermoFisher Scientific), respectively.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Demultiplexed FASTQ files were QC checked using FASTQC and processed using custom pipeline which involves read trimming, read alignment using bwa, filtering low-quality, unmapped and duplicated reads. BIGWIG files were generated using deeptools RPKM normalization.
Downstream analyses were performed in R (version 4.2.1) using various R packages.
Assembly: hg38
Supplementary files format and content: Tab-separated count matrix file and RPKM normalized bigwig files
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Michael Green |
| E-mail(s) |
mgreen5@mdanderson.org
|
| Phone |
713-745-4244
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Department of Lymphoma/Myeloma
|
| Street address |
7455 Fannin Street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE254902 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions [ca46_atac] |
| GSE254908 |
Smarca4 (Brg1) is a haploinsufficient B-cell tumor suppressor that fine-tunes centrocyte cell fate decisions |
|
| Relations |
| BioSample |
SAMN39748120 |
| SRA |
SRX23507650 |
