|
| Status |
Public on Mar 01, 2023 |
| Title |
RP tumor [JGAme_449_S WES] |
| Sample type |
SRA |
| |
|
| Source name |
sarcoma
|
| Organism |
Mus musculus |
| Characteristics |
genotype: p53 RP/-
background strain: 50% BALB/C - 50% C57BL6
tissue: sarcoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
mice with germline p53 alterations were sacrificed and tumors collected at end point
Library preparation followed standard Illumina protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
150nt
|
| Data processing |
library strategy: DNA-seq
fastq files were trimmed using trim_galore (0.6.5)
reads were aligned to genome using bwa mem (0.7.17)
cnv analysis carried out using gistic (2.0)
mutation call carried out using gatk (4.1.0.0)
Assembly: GRCm38
Supplementary files format and content: tab-deliminated segment mean
|
| |
|
| Submission date |
Dec 14, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Yuan Qi |
| E-mail(s) |
yqi1@mdanderson.org
|
| Organization name |
University of Texas M.D. Anderson Cancer Center
|
| Department |
Bioinformatics & Computational Biology
|
| Street address |
1400 Pressler St
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030-4008 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE220964 |
p53 dimers elicit unique tumor suppressive activities through an altered metabolic program [WES] |
| GSE220966 |
p53 dimers elicit unique tumor suppressive activities through an altered metabolic program |
|
| Relations |
| BioSample |
SAMN32232527 |
| SRA |
SRX18700843 |
