|
| Status |
Public on Mar 04, 2022 |
| Title |
C42_AKTI_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
C4-2 human PCa cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C4-2
cell type: Prostate cancer cell line
treatment: Akti
|
| Treatment protocol |
Cells were treated in DMEM for 72h with Akti and 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 nucleotides were removed from the sequenced reads using fastx_trimmer (FASTX Toolkit 0.0.13). The low quality nucleotides from the end of each read were removed using fastq_quality_trimmer (FASTX Toolkit 0.0.13) with -Q 33 -t 20 -l 25 parameters. Only the first sequenced read from 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: *txt: Htseq-count text files.
|
| |
|
| Submission date |
Dec 04, 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) |
| GSE162711 |
The androgen receptor-lncRNASAT1-Akt-p15 axis mediates androgen-induced cellular senescence in prostate cancer cells |
|
| Relations |
| BioSample |
SAMN17005129 |
| SRA |
SRX9634509 |
