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Sample GSM1778903 Query DataSets for GSM1778903
Status Public on Sep 01, 2018
Title LNCaP_2_GRCh37_74
Sample type SRA
Source name LNCaP, biological replicate 2
Organism Homo sapiens
Characteristics cell line: LNCaP
cell type: androgen-sensitive human prostate adenocarcinoma (LNCaP)
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 RNA was extracted using Trizol. Each sample was processed from cells cultured independently.
Libraries were prepared as per the manufacturers instructions using Illumina TruSeq kits with PolyA+ selection maintinaing strand informations and libraries were constructed at the Kinghorn Center for Clinical Genomics (The Garvan Institute of Medical Research, Darlinghurst, NSW, Australia).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description Genome-wide polyA+ transcript abundance of LNCaP cells.
Data processing Illumina software was used to generate fastq files. Before quantification Illumina adaptors were trimmed using Trim Galore version: 0.4.0 and Cutadapt version: 1.8.1 using the --paired flag.
A kallisto (version 0.42.1) index was created from all transcripts in ensembl GRCh37 build 74 downloaded from ensembl.
Each sample had transcript abundances quantified processed using kallisto quant (version 0.42.1)
Transcript abundances in transcripts per million were subsequently extracted using R (version 3.2.0) for downstream analysis.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Transcripts per million are presented for each sample per ensemble transcript ID in a comma delimited table.
Submission date Jul 02, 2015
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 GPL16791
Series (2)
GSE62410 Transcriptome profiling of Normal and Cancerous Prostate Cells
GSE70466 Replicated transcriptome profiling of Normal and Cancerous Prostate Cells [RNA-Seq]
BioSample SAMN03837858
SRA SRX1079399

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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