|
| Status |
Public on Mar 08, 2018 |
| Title |
RNA_control Sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2
tissue: Prostate
transfection: empty vector
|
| Treatment protocol |
no treatment
|
| Growth protocol |
C4-2 were routinely generated by regular cultures (typically 5 × 106 cells into a T75 flask) on uncoated plastic in RPMI1640 medium (Gibco, USA) supplemented with Charcoal stripped serum (Gibco, USA). Cells were transfected with empty vectors or BRD2/3/4 overexpressed vectors.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted as as described previously (Zhao Y, Wang L, Huang H, et al., Cell Rep. 2016).
Libraries were prepared according to Illumina's instructions accompanying the Total RNA-seq Sample Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using Tophat2 (v2.1.0) with default parameters.
RPKM and BIGWIG were calcualted using RSeQC (v2.3.6).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage signal
|
| |
|
| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
LIGUO WANG |
| E-mail(s) |
[email protected]
|
| Organization name |
Mayo Clinic
|
| Department |
Division of Computational Biology
|
| Street address |
200 1st St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE88872 |
SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer |
| GSE98010 |
SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRDs_OE_RNA-seq) |
|
| Relations |
| BioSample |
SAMN06768628 |
| SRA |
SRX2748856 |
