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Sample GSM2279608 Query DataSets for GSM2279608
Status Public on Mar 26, 2018
Title RNA-seq CAF3
Sample type SRA
Source name CAF
Organism Homo sapiens
Characteristics patient: 3
gender: Male
tissue: Prostate
cell type: Cancer Associated Fibroblast
Treatment protocol Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centifuged to create cell pellets. Cells were stored at -80°C until RNA extraction.
Growth protocol Prostate tissue was chopped into small pieces, approximately 2 mm3, and digested overnight at 37°C in RPMI containing 10% fetal calf serum (FCS), 25 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.5 mg/mL fungizone, 100 mg/mL gentamicin, 225 U/mL Collagenase Type I and 125 U/mL Hyaluronidase Type II (Sigma Aldrich) as previously described [PMID: 23558784]. Cell suspensions were seeded in RPMI containing 5% FCS, penicillin/streptomycin, 1 nM testosterone (Sigma Aldrich) and 10 ng/mL bFGF (Millipore), a medium that selects for fibroblasts compared to other prostatic cell types. Cells were grown at 37°C in a humidified incubator with 5% O2 and 5% CO2. The first passage of cells typically reached confluency within 2 weeks. The cells were used between passages 2-6.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase I digestion. RNA concentration and integrity was assessed on an Agilent Bioanalyzer 2100 using the Eukaryote Total RNA Nano Chip (Agilent). RNA (500 ng) was depleted of ribosomal RNA using RiboZero (Illumina, CA, USA).
Library preparation was performed for each sample using the Illumina TruSeq Stranded Total RNA sample kit (Illumina, CA, USA) according to the manufacturer’s protocol. TruSeq directional paired-end sequencing with 75bp chemistry was performed with six samples multiplexed per lane.
RiboZero RNA-seq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description CAF3
Data processing 75bp paired-end reads for 4 pairs of patient-matched CAF and NPF cells were processed using Trim Galore (version 0.2.8) for adapter trimming, Tophat (version 2.0.10) [PMID: 23618408] for mapping reads and Cufflinks (version 2.0.10) [PMID: 20436464] to assemble transcripts, both guided by GENCODE annotations (version 19) [PMID: 22955987]. Uniquely mapped properly paired reads were unambiguously assigned to exons of GENCODE genes (version 19) and counted using ht-seqcount (version 0.5.4p3) [PMID: 25260700], reads mapping to known rRNA loci were discarded using samtools procedures [PMID: 19505943].
Genome_build: hg19
Supplementary_files_format_and_content: file of counts data generated from Htseq count
Submission date Aug 15, 2016
Last update date May 15, 2019
Contact name Ruth Pidsley
Organization name Garvan Institute of Medical Research
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platform ID GPL16791
Series (2)
GSE85606 Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [RNA-seq]
GSE86260 Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype
BioSample SAMN05574751
SRA SRX2023081

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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