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Sample GSM1533839 Query DataSets for GSM1533839
Status Public on Sep 01, 2018
Title PrEC, rep1 [RNA-Seq]
Sample type SRA
Source name normal prostate epithelial cells (PrEC)
Organism Homo sapiens
Characteristics cell line: PrEC
tissue: Normal
Treatment protocol Untreated.
Growth protocol LNCaP cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum. PrEC cells were grown at 37ºC with 5% CO2 in PREGM media (Cambrex).
Extracted molecule polyA RNA
Extraction protocol Poly A+ Illumina TruSeq
RNA was extracted using Trizol and libraries prepared as per the manufacturers instructions and libraries were constructed at the Next Generation Genome Sequencing Facility (University of Western Sydney, Hawkesbury, NSW, Australia).
Illumina TruSeq (unstranded) with PolyA selection.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description sample_id: q2_0
Data processing Illumina software (version 1.9) was used to generate fastq files.
Sequenced reads were trimmed for adaptor sequence using trimgalore.
Trimmed reads were mapped using tophat with the parameter --library-type "fr-un-stranded" and raw counts for properly paired reads uniquely mapping to exonic regions of gencode genes (version 19) were obtained using ht-seq-count as implemented in the NGSANE framework (version 0.5.0).
Novel transcripts were assmebled using cufflinks and expression of genes and transcripts quantified using cuffquant and cuffnorm as implemented in the NGSANE framework (version 0.5.0).
Software used to process data (with version in brackets): igvtools(2.3.23), pigz(2.3), picard-tools(1.121), boost (1.53.0), samstat(1.08), java (jdk1.7.0_45), bedtools(2.19.1), python (2.7.3), bowtie (2.2.3), R (3.0.0), tophat (2.0.13), samtools (1.1), bedtools (2.19.1), pigz (2.3), htseq-count (0.6.1p1), cufflinks (2.2.1) and ImageMagick (6.8.5-8).
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited text files include raw counts of uniquely mapped properly paired reads for Gencode 19 genes.
Supplementary_files_format_and_content: Tab-delimited files generated by cuffnorm including for genes, transcripts, TSS groups, and CDS groups as described in the cufflinks manual. Transcripts assembled by cufflinks are provided as a GTF.
Submission date Oct 29, 2014
Last update date May 15, 2019
Contact name Timothy John Peters
Phone +61292958325
Organization name Garvan Institute of Medical Research
Department Immunology
Lab Immunogenomics
Street address 384 Victoria St
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platform ID GPL18460
Series (2)
GSE62410 Transcriptome profiling of Normal and Cancerous Prostate Cells
GSE62818 Transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]
BioSample SAMN03151552
SRA SRX746184

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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