|
| Status |
Public on Feb 06, 2016 |
| Title |
3045-NA NE |
| Sample type |
SRA |
| |
|
| Source name |
NEPC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Prostate
disease state: neuroendocrine prostate cancer
|
| Growth protocol |
Tumors were grown in NSG mice for 6-10 weeks prior to harvest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were embedded and frozen in OCT freezing compound. Frozen sections were mounted on laser capture microdissection slides and stained with the Arcturus Histogene Frozen Section Staining Kit. Laser capture microdissection of tumor regions was performed on a Leica Microsystems LMD7000. RNA was isolated with the Arcturus PicoPure RNA Isolation Kit.
cDNA libraries were prepared from Illumina RNA using the TruSeq RNA Sample Prep Kit v2 per manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina CASAVA 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to UCSC hg19 using MapSplice software.
Gene expression was quantified using RSEM and quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include normalized RSEM quantification for each sample.
|
| |
|
| Submission date |
Feb 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
John K Lee |
| E-mail(s) |
jklee5@fredhutch.org
|
| Phone |
206-667-6819
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Human Biology Division
|
| Lab |
Lee Lab
|
| Street address |
1100 Fairview Ave N, E2-112
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE77624 |
Expression profiling by high throughput sequencing of tumors derived from human prostate epithelial cells transformed with the oncogenes N-Myc and myrAKT1. |
|
| Relations |
| BioSample |
SAMN04461520 |
| SRA |
SRX1563503 |
