|
| Status |
Public on Sep 01, 2018 |
| Title |
PrEC_1_GRCh37_74 |
| Sample type |
SRA |
| |
|
| Source name |
PrEC, biological replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PrEC
cell type: normal prostate epithelial cells (PrEC)
|
| 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 PrEC 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 |
| E-mail(s) |
t.peters@garvan.org.au
|
| 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] |
|
| Relations |
| BioSample |
SAMN03837860 |
| SRA |
SRX1079401 |
