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| Status |
Public on Aug 02, 2018 |
| Title |
VCaP shERG 1 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
VCaP shERG
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| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP (CaP)
cell type: Prostate cancer cell line
infected with: shERG
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| Treatment protocol |
Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). Cells were harvested following 48h exposure to lentivirus and either 2 days (SW13), 4 days (LNCaP) or 8 days (VCaP) of selection. The overexpression constructs used in LNCaP cell experiments were selected with blasticidin. The knockdown constructs used in VCaP cell experiments were selected with puromycin. SW13 cells were selected with both blasticidin and puromycin as the empty and V5-ERG vectors were blasticidin resistant, while the V5-luciferase, V5-BRG1 and V5-BRG1 K785R constructs were puromycin resistant. RNA-seq samples were prepared in duplicate with independent infection, selection and cell culture.
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| Growth protocol |
All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10-20% fetal bovine serum, 1% Glutamax (Gibco), 1% Sodium Pyruvate (Gibco) and 1% Penicillin-Streptomycin (Gibco).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
All RNA was produced using the RNeasy Mini Kit (Qiagen).
All library prep and sequencing were 75bp single end on Illuminia Nextseq 500
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
VCaP shERG 1 RNA-seq
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| Data processing |
RNA-seq reads were mapped to the human reference genome (hg19) using STAR(Dobin et al., 2013) version 2.3.1 with default parameters.
RPKM values for biological duplicate RNA-seq samples were generated using GFold(Feng et al., 2012) version 1.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: read_cnt containing GeneSymbol, GeneName, Read Count, Gene Exon Length, RPKM columns
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| Submission date |
Feb 15, 2018 |
| Last update date |
Aug 02, 2018 |
| Contact name |
Cigall Kadoch |
| Organization name |
Dana-Farber Cancer Institute
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| Department |
Pediatric Oncology
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| Lab |
Kadoch Lab
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| Street address |
450 Brookline Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE110656 |
Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. [RNA-seq] |
| GSE110657 |
Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. |
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| Relations |
| BioSample |
SAMN08541436 |
| SRA |
SRX3702034 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3005044_VCaP_shERG_1.read_cnt.txt.gz |
270.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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