|
| Status |
Public on Aug 01, 2016 |
| Title |
LNCaP vehicle treatment |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP vehicle 24h treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP cells
cell type: prostate cancer
|
| Treatment protocol |
Cells were treated with siControl or siAR (10 nM) for 48 h and then treated with Et or 10 nM dihydrotestosterone (DHT) for 24 h.
|
| Growth protocol |
LNCaP cells were cultured in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days. VCaP cells were cultured in DMEM containing 10% FBS. Before hormone treatment, cells were incubated in DMEM containing 2.5% charcoal/dextran treated FBS for three days. LTAD and VCaP -LTAD cells were cultured in phenol red free medium supplemented with 10 % charcol dextran treated FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using ISOGEN reagent.
RNA sequencing (RNA-seq) library construction and sequencing was performed according to the manufacturer’s protocol (OP-Hiseq2000-sequencing-cBot-v3.0.) for hiseq2000.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The illumina hiseq2000-generated RNA-Seq reads was in 50 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the human Noncode v4 or GENCODE v19 lncRNA database.
The expression levels of mapped transcripts were normalized into transcript parts per kilobase of exon model per million mapped reads (PRKM) to faciliate comparison among different samples.
Genome_build: hg19
|
| |
|
| Submission date |
Jun 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ken-ichi Takayama |
| Organization name |
Tokyo Metropolitan Institute of Gerontology
|
| Street address |
Sakaecho
|
| City |
Itabashi-ku |
| ZIP/Postal code |
173-0015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE82223 |
Investigation of androgen-regulated lncRNAs in prostate cancer cells |
| GSE82225 |
Androgen-induced lncRNA SOCS2-AS1 Promotes Cell Growth and Inhibits Apoptosis in Prostate Cancer Cells |
|
| Relations |
| BioSample |
SAMN05201375 |
| SRA |
SRX1818766 |
