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Sample GSM1845862 Query DataSets for GSM1845862
Status Public on Feb 09, 2017
Title 2,8-18 RNA-seq
Sample type SRA
Source name from prostate cancer lymph node metastasis
Organism Homo sapiens
Characteristics cell line: ATCC CRL-1740
cell type: LNCaP
passages: 33 (in our lab)
treatment: Treated R1881 10 nM 48 hrs
Growth protocol All cells were grown as monolayers in 6-well plates using standard and published growth conditions (QU, Y (2013) Cancer Research Dec 1;73(23):7090-100 for EP156T and EPT3-M1 and according to the ATCC recommendation for LNCaP, 22RV1 and VCaP cells). For experiments media in the wells were adjusted to the indicated concentrations and for the given time with synthetic androgen R1881 or DMSO vehicle for negative controls.
Extracted molecule total RNA
Extraction protocol Cells were harvested by adding 700 microliters Trizol lysis buffer to each 6-well immediately following removal of growth medium. Total RNA was purified following the Qiagen miRNeasy protocol followed by DNAse treatment of total RNA.
Total RNA was treated according to STARSeq roitines (2014), including Agilent Bioanlyzer2100, all RIN values >10, rRNA depletion, cDNA synthesis, concentration and quality control (Qubit/Agilent Bioanalyzer), fragmentation and sizing (Covaris TMS2), sequencing preparation with barcoded adapters for muliplexing and Illumina NextSeq 500 sequencing, paired end read, 150 nt, 100 Mio reads.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Base calling and quality scoring are performed by an updated implementation of Real-Time Analysis (RTA), called RTA v2
TopHat2 v2.0.7
Cufflinks 2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: cufflinks output files, gene expression in fpkm
Submission date Aug 06, 2015
Last update date May 15, 2019
Contact name Biaoyang Lin
Organization name ZheJiang University
Department ZCNI
Lab Systems Biology Division
Street address 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.
City HangZhou
ZIP/Postal code 310058
Country China
Platform ID GPL18573
Series (1)
GSE71797 Genome-wide RNA-sequencing (RNA-seq) of benign and malignant prostate cell lines without and with androgen (R1881) stimulation.
SRA SRX1134928
BioSample SAMN03979005

Supplementary file Size Download File type/resource
GSM1845862_2-8-18.genes.fpkm_tracking.gz 813.4 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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