|
| Status |
Public on May 11, 2017 |
| Title |
pten.nTg.3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse prostate
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: prostate
pten: WT
trap1: non-transgenic
replicate: 3
|
| Treatment protocol |
Twelve RNA samples extracted from Tg prostates were first treated with Invitrogen/Ambion DNA-free-kit (cat #AM1906) to remove DNA
|
| Growth protocol |
A Pten heterozygous male mouse (http://www.ncbi.nlm.nih.gov/pubmed/9990064) was used in a breeding pair with a TRAP1 transgenic female mouse (line 810). Of the resulting offspring, 25% of the animals were used for further experiments (PTen het-Tg male mice constituted the experimental group, while PTen het-non Tg male mice were used as control group)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol
The sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA sequencing library preparation kit (SKU:015.24) for Illumina sequencing platform compatible libraries. All 12 libraries were pooled in equal molar amounts and run on the Illumina Nextseq500 using the Mid Output V2 (150 cycles) kit (cat # FC-404-2001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq for pten WT mouse, non-transgenic Trap1 replicate 3
|
| Data processing |
RNA-Seq data analysis was done with rsem(ver. 1.2.3) and mm10 genome with UCSC known gene set.
Two samples were removed as technical outliers based on Principal Component Analysis.
DESeq2 was used for differential expression was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed file contains raw counts for all genes
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE81316 |
Transgenic Expression Of Mitochondrial Chaperone Trap1 Accelerates Prostate Cancer Development |
|
| Relations |
| BioSample |
SAMN04978790 |
| SRA |
SRX1756480 |
