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Sample GSM1863098 Query DataSets for GSM1863098
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
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
BioSample SAMN04017475
SRA SRX1167168

Supplementary file Size Download File type/resource
GSM1863098_20140507_C4_2B_Vehicle_gene_RPKM.txt.gz 221.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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