|
| Status |
Public on Jan 27, 2020 |
| Title |
4970_2_gNT_UT_R2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP_sgNT UT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer cell line
genotype/variation: control (sgNT)
treatment: vehicle for 5 days
|
| Treatment protocol |
Cells were plated (500 000 cells / 10cm dish) in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2. Next day, enzalutamide (10 uM) or vehicle was added, and cells were cultured for 5 days (medium was refreshed daily) before harvesting using Trizol.
|
| Growth protocol |
LNCaP cells harboring CRISPR constructs were cultured in RPMI (+10% FBS, +1% pen/strep) at 37C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using Trizol
Stranded RNA libraries were prepared for sequencing according to Illumina instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
gNT_UT_R2_ATTCCTT
|
| Data processing |
Deseq2 was used for RNA-seq data normalization.
The differential expression was based on the ratio of normalized read counts (FPKM, after library size correction).
An absolute fold-change threshold of 2 was used. Genes with a coverage <50 in both conditions were excluded from the analyses to prevent spurious results.
Genome_build: hg38
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples
|
| |
|
| Submission date |
Apr 24, 2019 |
| Last update date |
Jan 27, 2020 |
| Contact name |
Sander Palit |
| E-mail(s) |
[email protected]
|
| Organization name |
Netherlands Cancer Institute
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE130246 |
RNA-seq control (sgNT) and TLE3KO (sgTLE3) cells treated with 10 uM enzalutamide or vehicle |
|
| Relations |
| BioSample |
SAMN11490484 |
| SRA |
SRX5729230 |
