|
| Status |
Public on Dec 25, 2019 |
| Title |
LNCAP_2B9_SHRNA_1 |
| Sample type |
SRA |
| |
|
| Source name |
Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
shRNA: HNRNPM targetting shRNA (2B9)
cell type: Epithelial cells
cell line: LNCaP
|
| Treatment protocol |
LNCAP cells were infected at ~MOI1 with lentiviruses (PLKO.1) expressing control non-targetting shRNA (SCR) or HNRNPM specific shRNA (2B7 and 2B9). Virus infected cells were then selected in puromycin containing media (1ug/ml) after a 2 day infection. After selection was completed, cells were harvested for RNA isolation.
|
| Growth protocol |
LNCAP cells were maintained in in RPMI media supplemented with 10% fetal bovine serum (FBS; Lonza) 1mM sodium pyruvate (Gibco, 11360070), non-essential amino acids (Gibco; 11140050) and 50U/ml Penicillin-Streptomycin (Gibco, 15140163).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from shRNA treated LNCAP cells using the Purelink RNA Mini Kit (Thermo Fisher Scientific; 12183018A)in conjunction with Trizol Reagent (Invitrogen; 15596018) following the manufacturer’s protocol.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Sequenced reads were mapped to hg19 whole genome using STAR version 2.4.2a with default parameters
FPKM and differential expression were calculated using the Cufflinks suite version 2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 27, 2018 |
| Last update date |
Dec 25, 2019 |
| Contact name |
Diana HP Low |
| E-mail(s) |
dlow@imcb.a-star.edu.sg
|
| Organization name |
Institute of Molecular and Cell Biology
|
| Lab |
Chromatin, Epigenetics & Differentiation
|
| Street address |
#03-06, 61 Biopolis Drive, Proteos
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE113782 |
HNRNPM-regulated splicing dependencies in prostate cancer [RNA-Seq] |
| GSE113786 |
HNRNPM-regulated splicing dependencies in prostate cancer |
|
| Relations |
| BioSample |
SAMN08995367 |
| SRA |
SRX4004393 |
