|
| Status |
Public on Jul 12, 2022 |
| Title |
SPOP WT +DHT repeat 2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP prostate cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP prostate cancer cell line
genotype: Wildtype
media type: Hormone replete media
treatment: No treatment
|
| Treatment protocol |
All cells grown in hormone deprived media were transitioned to phenol red free and dextran-charcoal treated FBS containing media 10 days prior to RNA harvest. For all shGLI3 samples, cells were treated with shGLI3 lentivirus 6 days prior to transition to hormone deprived media.
|
| Growth protocol |
LNCaP were cultured at 37C and 5% CO2 in standard or phenol red–free RPMI-1640 medium containing 10% standard or dextran-charcoal treated fetal bovine serum respectively
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol and Direct-zol RNA Miniprep kit (Zymo Reserach) according to the manufacturer’s instructions.
Total RNA samples about 1-2 mg were used for sequencing library preparation according to Illumina TruSeq stranded mRNA-seq Sample Preparation Guide. Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SR) sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Wildtype LNCaP cells grown in hormone replete media
LNCaP_repl2
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling for samples by HiSeq2000, and Illumina bcl2fastq software used for base-calling for samples by HiSeq3000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Jul 22, 2019 |
| Last update date |
Jul 14, 2022 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE134682 |
Pathologically stabilized GLI3 promotes androgen-independent growth of SPOP mutant prostate cancer cells through reactivation of an AR signaling axis |
|
| Relations |
| BioSample |
SAMN12339754 |
| SRA |
SRX6489943 |
