|
| Status |
Public on Mar 08, 2016 |
| Title |
20140507 C4-2B vehicle |
| Sample type |
SRA |
| |
|
| Source name |
C4-2B cells cultured in medium with vehicle control.
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2B prostate cancer cell line
cell type: Bone metastatic LNCaP-derivative
agent: control
|
| Treatment protocol |
C4-2B cells were seeded into 6 well plate and cultured in CRPC medium (RPMI 1640, 9%cds-FBS and 1% regular FBS, L-Glutamine, Pen-Strep), next day, cell were then treated with vehicle or SR2211 (5µM) or E11/XY011 (5µM) for another 48 hours.
|
| Growth protocol |
C4-2B cells were cultured in RPMI supplemented with 10% FBS for maintenance or 9% cds-FBS and 1% regular FBS (to mimic the CRPC condition) for experiments. Cells were grown at 37℃ in 5% CO2 incubators.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from C4-2B cells treated with Vehicle, SR2211 or XY018 for 48 hours.
RNA-Sequencing (RNA-Seq) libraries were prepared from 1 μg total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. Briefly, poly-adenylated mRNA was purified from total RNA and rRNA removed by two rounds of binding to magnetic poly-T beads. This was followed by RNA fragmentation by incubation in the presence of divalent cations at 94ºC for 5 minutes. Double-stranded cDNA was generated by random-primed first-strand synthesis with SuperScript II reverse transcriptase and subsequent second strand synthesis with RNase H and DNA Polymerase I. The cDNA was then blunt-ended with T4 and Klenow DNA polymerases to remove 3′-overhangs and fill in 5′-overhangs, phosphorylated with T4 PNK, and then 3′-A tailed by incubation with Klenow Fragment (3´→5´ exo–) and dATP. Illumina paired-end (PE) adapters were ligated, followed by purification wit AMPure XP beads. The library was enriched by high-fidelity PCR amplification (15 cycles) with Phusion DNA Polymerase (Finnzymes Oy) and adapter-specific primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
sequence reads were mapped to the reference human genome assembly (Feb. 2009,GRCh37/hg19) with BWA and Bowtie software.
the Cufflinks package was applied for transcript assembly, quantification of normalized gene and isoform expression in RPKM (Reads per kilobase per million mapped reads) or FPKM (fragments per kilobase of exon per million fragments mapped), and testing for differential expression (Cuffdiff).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID, symbol and FPKM or RPKM values for each gene and were prepared from the Cufflinks output files (tracking).
|
| |
|
| Submission date |
Aug 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Junjian Wang |
| E-mail(s) |
jjwang@ucdavis.edu
|
| Phone |
9167343221
|
| Organization name |
UC Davis
|
| Department |
Biochemistry and molecular medicine
|
| Street address |
rm1204, Res3, 4645 2nd Ave
|
| City |
Sacramento |
| State/province |
california |
| ZIP/Postal code |
95817 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE72483 |
ROR-γ drives androgen-receptor expression and represents a therapeutic target in castration-resistant prostate cancer |
|
| Relations |
| BioSample |
SAMN04017475 |
| SRA |
SRX1167168 |
