|
| Status |
Public on Jun 10, 2023 |
| Title |
Y CHROMOSOME positive cell line |
| Sample type |
SRA |
| |
|
| Source name |
MB49
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MB49
cell type: bladder cancer cell line
genotype: Y positive
|
| Growth protocol |
MB49 bladder cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from parental, Y-, and Y+ MB49 cell lines by Invitrogen Kit (catalog No K1820) according to the manufacturer’s instructions
The genomic DNA was randomly sheared into short fragments, end-repaired, A-tailed, and ligated with Illumina adapters. After PCR amplification, size selection, and purification, we proceeded with the hybridization capture of libraries. The captured libraries were enriched by PCR amplification and checked with Qubit and bioanalyzer for quality control. The libraries were then pooled and sequenced on Illumina platforms using the PE150 strategy.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
MBN
|
| Data processing |
We mapped the paired-end clean reads to the mouse reference genome (Mouse, NCBI37/mm9) using BWA, sorted them with Sambamba, and marked duplicates with Picard.
Finally, we computed the coverage and depth, and tested for SNP and InDel detection.
Assembly: mm10
Supplementary files format and content: tab-delimited text files contain annotation information for INDELs
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Jun 10, 2023 |
| Contact name |
Hany A Abdel-Hafiz |
| E-mail(s) |
hany.abdel-hafiz@cshs.org
|
| Organization name |
Cedars-Sinai Medical Center
|
| Department |
Medicine/ Medical Oncology
|
| Street address |
110 N George Burns RD, DRoom 3057
|
| City |
los Angeles |
| State/province |
California |
| ZIP/Postal code |
90036 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE230819 |
Y chromosome loss in bladder cancer contributes to T cell exhaustion and sensitivity to immune checkpoint blockade [WES] |
| GSE230820 |
Y chromosome loss in cancer drives growth by evasion of adaptive immunity |
|
| Relations |
| BioSample |
SAMN34412902 |
| SRA |
SRX20122717 |
