|
| Status |
Public on Sep 03, 2019 |
| Title |
CM3: LNCaP_sicontrol_MDV |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
tissue: Prostate adenocarcinoma
sirna: siControl (Dharmacon, Cat#D-001810-10-50)
treatment: Enzalutamide
replicate: Biological replicate 3
|
| Treatment protocol |
For all experiments, cells transfected with either non-targeting control siRNA or siGATA2 were maintained in phenol red-free RPMI medium with 5-10% charcoal-stripped FBS for 3 days before treatment. Then cells were treated with vehicle, DHT and MDV for indicated time.
|
| Growth protocol |
The prostate cancer cell line LNCaP was cultured in the RPMI complete medium (10% FBS).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the mRNA was recovered for library generation.
For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 4000 at the Duke sequencing core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq process: The RNA-seq data was aligned by TopHat 2.0. Reads were mapped to the reference genome build (hg19). Read counts were calculated with Partek. The reads count in exon regions was used to estimate the expression level of the genes.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include read counts of all genes for each Sample.
|
| |
|
| Submission date |
Aug 07, 2019 |
| Last update date |
Sep 03, 2019 |
| Contact name |
Zhong Chen |
| E-mail(s) |
zhong.chen128@duke.edu
|
| Organization name |
Duke University
|
| Department |
Pathology
|
| Lab |
Room 1027B, GSRB1
|
| Street address |
905 S. LaSalle Street
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE125014 |
Molecular determinants for enzalutamide-induced transcription in prostate cancer |
|
| Relations |
| BioSample |
SAMN12512951 |
| SRA |
SRX6664861 |
