|
| Status |
Public on Mar 04, 2022 |
| Title |
LNCAP_SAL_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP human PCa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: Prostate cancer cell line
treatment: 1nM R1881
|
| Treatment protocol |
Cells were treated in DMEM for 72h with DMSO or 1nM R1881(SAL) or 1pM R1881(LAL).
|
| Growth protocol |
Cells were cultured in 5% FBS DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using peqGOLD TriFast (Peqlab, Erlangen, Germany) according to the manufacturer’s protocol.
Sequencing library was prepared using SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian (TAKARA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Transcriptional profiling (RNA sequencing)
|
| Data processing |
The first 4 nucleotide was removed from the sequenced reads using fastx_trimmer (FASTX Toolkit 0.0.13). The low quality nucleotides from the end of each read was removed using fastq_quality_trimmer (FASTX Toolkit 0.0.13) with -Q 33 -t 20 -l 25 parameters. Only the first sequenced read form the pair end (R1) was used for the downstream analysis.
The fastq files were mapped to the hg19 genome using tophat (v2.1.0) with the following parameters --bowtie1 --no-coverage-search -a 5.
The number of reads covered by each gene was calculated using htseq-count (0.11.2) with -s no -a 0 -t exon -m intersection-nonempty parameters and hg19 gencode.v19 annotation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq-count text files.
|
| |
|
| Submission date |
Aug 01, 2020 |
| Last update date |
Mar 04, 2022 |
| Contact name |
Seyed Mohammd Mahdi Rasa |
| E-mail(s) |
[email protected]
|
| Phone |
015258164616
|
| Organization name |
Universitätsklinikum Schleswig-Holstein
|
| Department |
Institut for Immunology
|
| Lab |
Immunology (Prof. Sheffold)
|
| Street address |
Michaelisstrasse 5
|
| City |
Kiel |
| State/province |
Schleswig-Holstein |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE155528 |
Opposite response of hTERT expression by androgen dose: Androgen-mediated inhibition of hTERT is mediated by the ING1 and ING2 tumor suppressors in prostate cancer cells |
|
| Relations |
| BioSample |
SAMN15693639 |
| SRA |
SRX8863970 |
