|
| Status |
Public on Jan 01, 2015 |
| Title |
Tamoxifen Rep #1 |
| Sample type |
SRA |
| |
|
| Source name |
Cecal GIST tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Cecal GIST tumor
genotype: Kit V558Delta/+; Etv1 flox/flox; Rosa26 CreERT2/CreERT2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
GIST tumors from the cecums of mice were explanted and grounded in 1000 μl Trizol (Invitrogen) using a PowerGen homogenizer (Fisher Scientific), followed by addition of 200 μl chloroform. The samples were then centrifuged at 10,000g for 15 min. The upper phase was mixed with an equal volume of 70% ethanol, and the RNA was further purified using E.Z.N.A total RNA kit (Omega).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ECK1773
|
| Data processing |
The sequenced reads from fastq files were mapped to mm9 using STAR version 2.3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cuffdiff from the Cufflinks suite (Trapnell Nature biotechnology), using upper quartile normalization.
RPKM of all 8 samples were combined into a single file.
Genome_build: mm9
|
| |
|
| Submission date |
Dec 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
|
| Phone |
646-888-3356
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Chen
|
| Street address |
1275 York Ave, Box 20
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE64608 |
RNA-Seq of murine GIST-like tumors after Etv1 ablation |
|
| Relations |
| BioSample |
SAMN03274270 |
| SRA |
SRX825979 |
