|
| Status |
Public on Dec 05, 2019 |
| Title |
IR+ Dox- 1R |
| Sample type |
SRA |
| |
|
| Source name |
Prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-shPRMT5
treatment: Dox-
genotype/variation: No knockdown
stress: 2 Gy radiation
|
| Treatment protocol |
LNCaP-shPRMT5 cells were seeded on 10 cm dishes and Doxycyline (Dox) was applied at the final concentration of 1 µg/mL every 48 hours to establish and maintain PRMT5 knockdown. For the IR+ group, cells were then subjected to 2 Gy IR and cells were harvested 24 h following IR treatment.
|
| Growth protocol |
LNCaP-shPRMT5 cells were cultured in RPMI1640 medium with 10% fetal bovine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol Reagent (Ambion, Carlsbad, CA, USA). Total RNA was reverse transcribed into cDNA and cDNA was used as template for RNA-seq analysis.
Library Construction RNA polyA+
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
irradiation.counts
Sample 7
|
| Data processing |
Base calling and quality scoreing were performed in Illumina HiSeq (sample 7 to sample 10)/Illumina MiSeq (sample 1 to sample 6).
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to Gencode 25 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GENCODE 25 GRCh38
Supplementary_files_format_and_content: Raw counts
|
| |
|
| Submission date |
Mar 09, 2018 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Chang-Deng Hu |
| E-mail(s) |
hu1@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Medicinal Chemistry and Molecular Pharmacology
|
| Street address |
201 S. University St, Hansen Life Sciences Building, Room 401A
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE111620 |
RNA-seq analysis of PRMT5-regulated genes in irradiated/non-irradiated LNCaP cells |
|
| Relations |
| BioSample |
SAMN08667789 |
| SRA |
SRX3777466 |
