|
| Status |
Public on Dec 22, 2023 |
| Title |
22Rv1_4A_Control_1 |
| Sample type |
SRA |
| |
|
| Source name |
22Rv1
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Prostate cancer
gender: male
repository source fibroblast id: 22Rv1 (ATCC)
|
| Treatment protocol |
DU145, 22Rv1 and ARCaPM, were collected after 48 hours of being transfected with siRNA control or two siRNAs targeting MITF.
|
| Growth protocol |
Prostate cancer DU145, 22Rv1, and ARCaPM were obtained from ATCC and Novicure grown in RPMI media with 10% FBS in a humidified 37°C atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini kit (QIAGEN) in accordance with manufacturer’s instructions.
High-quality total RNA samples (RNA Integrity score > 8 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol. The libraries were sequenced by HiSeq 2500 genome sequencer (Illumina) to generate 100 bp single-end reads.
Hi-Seq, 100nt, Single-End Read, 4 samples per lane
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
4A
|
| Data processing |
The Illumina TruSeq RNA kit was used for 100nt/single end reads, 4 samples were run per lane using the standard Truseq indices. Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx format; the read count for each gene
|
| |
|
| Submission date |
Jul 08, 2019 |
| Last update date |
Dec 22, 2023 |
| Contact name |
Yujin Hoshida |
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE133977 |
Role of MITF in advanced lethal prostate cancer |
|
| Relations |
| BioSample |
SAMN12232243 |
| SRA |
SRX6416596 |
