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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 09, 2017 |
| Title |
7,3-19 RNA-seq |
| Sample type |
SRA |
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| Source name |
from prostate cancer vertebral metastasis
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| Organism |
Homo sapiens |
| Characteristics |
cell line: ATCC CRL-2876
cell type: VCaP
treatment: Treated with 1 nM R1881 24 hrs
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Aug 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Biaoyang Lin |
| Organization name |
ZheJiang University
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| Department |
ZCNI
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| Lab |
Systems Biology Division
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| Street address |
866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.
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| City |
HangZhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| 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. |
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| Relations |
| SRA |
SRX1134935 |
| BioSample |
SAMN03979012 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1845869_7-3-19.genes.fpkm_tracking.gz |
844.6 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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