|
| Status |
Public on Apr 07, 2021 |
| Title |
2418-2_P4_SQ [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Mouse tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: PbCre/+; Pten f/f; NMYC/NMYC; Rb1 f/f
age: 13 weeks
tissue: Mouse tumor
status: Intact
pathology: Squamous
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from GEM prostate tumors was performed using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega, AS1280). Regions of the cryopreserved tumor samples that were identified by a blinded pathologist were excised with a biopsy punch and processed as described.
Libraries were generated using the TruSeq RNA Library Prep Kit [Non-stranded, polyA+] (Illumina) following the manufacturer's recommended protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
11_2418-2_P4_SQ_S11
|
| Data processing |
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to mm10 using STAR
BAM file creation, sorting, and indexing were performed using SAMtools
Transcript abundances in FPKM were caluculated using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: Transcript abundances in FPKM calculated using Cufflinks in comma-separated values (CSV) format
|
| |
|
| Submission date |
Sep 23, 2020 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Nicholas Brady |
| E-mail(s) |
njb2003@med.cornell.edu
|
| Organization name |
Weill Cornell Medicine
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
1188 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE151426 |
Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer |
| GSE158467 |
Temporal evolution of cellular heterogeneity during the progression to advanced, AR-negative prostate cancer [RNA-seq] |
|
| Relations |
| BioSample |
SAMN16249751 |
| SRA |
SRX9180458 |
