|
| Status |
Public on Oct 01, 2022 |
| Title |
R597-3-245-T5 |
| Sample type |
SRA |
| |
|
| Source name |
mammary tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mammary tumors
genotype: Trp53R245W/+
strain: C57BL/6J X BALB/cJ F1 hybrid
gender: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq stranded protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired-end reads in fastq format were initially checked for read quality using FastQC 0.11.8
Sequence reads were mapped to the mouse reference genome (Gencode GRCm38) using TopHat 2.1.1 (parameter: --library-type=fr-firststrand)
The BAM file with mapped reads for each sample was sorted and then used as an input for HTSeq 0.11.0 in order to generate read count data on gene level (parameters: -s reverse -m union)
Assembly: GRCm38
Supplementary files format and content: raw read count data generated by htseq-count 0.11.0 for each sample
|
| |
|
| Submission date |
Jul 06, 2022 |
| Last update date |
Oct 02, 2022 |
| Contact name |
Khandan Keyomarsi |
| E-mail(s) |
kkeyomar@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Experimental Radiation Onc
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE207604 |
Omics analyses of a somatic Trp53R245W/+ breast cancer model identify cooperating driver events activating PI3K/Akt/mTOR signaling |
|
| Relations |
| BioSample |
SAMN29543217 |
| SRA |
SRX16046580 |
