|
| Status |
Public on Oct 29, 2021 |
| Title |
RNASeq_VCaP_FBS_siMYC_1094_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
VCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
cell type: prostate cancer
genotype: MYC knockdown, siMYC #1094
treatment: FBS medium
|
| Treatment protocol |
For androgen-starving conditions, cells were grown in medium containing CDS (charcoaldextran stripped serum, from Hyclone). Plasmids and siRNA transfections were carried out using the Lipofectamine 2000 (Invitrogen), following the manufacturer’s directions.
|
| Growth protocol |
LNCaP were grown in RPMI-1640 containing 10% FBS (GIBCO, 10437-028); LNCaP cell line overexpression of Flag-tagged AR (LNCaP-AR, or LA) was based on LNCaP cells infection with lenti-viral AR expression vector and selected on hygromycin B (200ug/ml); VCaP cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) medium containing 10% FBS.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy MiniKit (74106, Qiagen) following manufacturer’s procedure.
Whole transcriptome sequencing libraries were prepared using TruSeq® Stranded mRNA Library Prep Kit (RS-122-2101, Illumina, San Diego, CA, USA) by following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNASeq_VCaP_FBS_siMYC_1094_rep2
RNASeq_expression_2.txt
|
| Data processing |
Sequencing reads were aligned to hg19 human genome using STAR (version 2.4.2a). Reads per kilobase per million mapped reads (RPKM) was then calculated based on gene read count and GENCODE v24 GRCh37 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain the gene expression matrices
|
| |
|
| Submission date |
Dec 10, 2020 |
| Last update date |
Oct 29, 2021 |
| Contact name |
Haiyang Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
UNIV HEALTH NETWORK
|
| Department |
Princess Margaret Cancer Centre
|
| Lab |
Housheng Hansen He
|
| Street address |
101 College Street, 11-601D, TMDT, 11-601D, TMDT
|
| City |
TORONTO |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE157104 |
The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry (RNA-Seq) |
| GSE157107 |
The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry |
|
| Relations |
| BioSample |
SAMN17052283 |
| SRA |
SRX9670540 |
