|
| Status |
Public on Feb 07, 2019 |
| Title |
Sample_OEvehicle2 |
| Sample type |
SRA |
| |
|
| Source name |
PC-3
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: overexpression vehicle
cell line: PC-3
cell type: prostate cancer cell line
|
| Treatment protocol |
For knockdown, The shRNA expressing lentiviral transfer vector was transfected together with the packaging (psPAX2) and envelope plasmid (pMD2.G) by lipo3000. The medium was harvested at 24 and 48 hours after transfection before storing at -80 °C. For infection, 5 x 104 cells were seeded per well in six-well plates and infected with lentivirus on the next day. Infected cells were selected with 3 μg/mL puromycin. For overexpression, PCa cells were transfected with 1.2 μg circRNA overexpressing plasmids or empty vector by lipo3000 transfection reagent (Invitrogen, USA) as per the manufacturer’s protocol. The transfected cells were harvested 24 hours after transfection for RNA extraction or other assays.
|
| Growth protocol |
PCa cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were cleaned-up by phenol-chloroform before resuspension in a small volume of RNase-free H2O.
RNA-Seq library for circCSNK1G3 was constructed with the kit from Illumina (TruSeq Stranded mRNA Library Prep Kit) according to the manufacturer’s protocol. RNA-Seq libraries were sequenced as single-end reads in duplicates at ~30 million reads per library using HiSeq 2000 platforms.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 2
|
| Data processing |
RNA-Seq reads were mapped to GRCh37 with Gencode v24lift37 annotation using STAR (v2.5.3a), the GeneCounts parameter was set to quantMode to get raw counts on genes
edgeR(v3.12.1) was used for differential expression analysis
Genome_build: GRCh37
Supplementary_files_format_and_content: txt files for gene raw counts
|
| |
|
| Submission date |
Apr 13, 2018 |
| Last update date |
Feb 07, 2019 |
| Contact name |
Housheng Hansen He |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Toronto
|
| Lab |
He lab
|
| Street address |
101 College Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE113121 |
Overexpression and knockdown experiment for circCSNK1G3 |
| GSE113124 |
Widespread and Functional RNA Circularization in Localized Prostate Cancer. |
|
| Relations |
| BioSample |
SAMN08929702 |
| SRA |
SRX3933422 |
