|
| Status |
Public on Oct 10, 2021 |
| Title |
HT1912011246_VCaP_3h_COL04_S24_L002 |
| Sample type |
SRA |
| |
|
| Source name |
VCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: VCaP
cell type: Prostate cancer cell line
treatment: DHT
time: 3h
|
| Treatment protocol |
VCaP cells were transferred into phenol-red free DMEM media (Gibco), 1day prior to DHT stimulation. The media was supplemented with 10% charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or DHT at 4 time points (0h, 3h, 6h and 12 h), before being dissociated and triturated into single-cell suspensions for single-cell analyses.
|
| Growth protocol |
VCaP human prostate cancer cell lines were obtained from ATCC and maintained in DMEM media (Gibco). The media was supplemented with 10% fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nextera XT Index Kit v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
HT
PolyA RNA
processed data file: VCaP_HT_genes_fpkm.txt
|
| Data processing |
For processing the HT samples, demultiplexing was performed using Fluidigm’s HT Demultiplexer Perl script.
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKM values for each single cell.
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Oct 10, 2021 |
| Contact name |
Xin Chen |
| Organization name |
Guangdong University of Technology
|
| Street address |
No. 100 Waihuan Xi Road, GuangzhouHigher Education Mega Center, Panyu District
|
| City |
Guangzhou |
| ZIP/Postal code |
510006 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE145825 |
Single-cell RNA-seq analysis of prostate cancer cells [I] |
| GSE145845 |
Single-cell RNA-seq analysis of prostate cancer cells |
|
| Relations |
| BioSample |
SAMN14173683 |
| SRA |
SRX7793890 |
