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| Status |
Public on Sep 01, 2018 |
| Title |
PrEC, rep1 [RNA-Seq] |
| Sample type |
SRA |
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| Source name |
normal prostate epithelial cells (PrEC)
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| Organism |
Homo sapiens |
| Characteristics |
cell line: PrEC
tissue: Normal
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| Treatment protocol |
Untreated.
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| 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).
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
sample_id: q2_0
Sample name: RNA_SEQ_CSP_TGACCA
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| 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.
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| Submission date |
Oct 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Timothy John Peters |
| E-mail(s) |
t.peters@garvan.org.au
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| Phone |
+61292958325
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| Organization name |
Garvan Institute of Medical Research
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| Department |
Immunology
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| Lab |
Immunogenomics
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| Street address |
384 Victoria St
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| 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] |
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| Relations |
| BioSample |
SAMN03151552 |
| SRA |
SRX746184 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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