|
| Status |
Public on Feb 07, 2019 |
| Title |
PC-3_siCSNK1G3_1 |
| Sample type |
SRA |
| |
|
| Source name |
PC-3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate cancer cell line
cell line: PC-3
|
| 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 |
Total RNA from the cell-lines was purified with RNeasy Mini Kit (QIAGEN, Cat. #74106), and the DNA was digested by RNase-Free DNase Set (QIAGEN, Cat. #79254) during the RNA purification.
RNA-Seq libraries for circCSNK1G3, circGOLPH3, circSTAU2 and CSNK1G3 were constructed with the kit from Illumina (TruSeq Stranded mRNA Library Prep Kit) according to the manufacturer’s protocol. RNA-Seq libraries were sequenced as paired-end reads in duplicates at ~30 million reads per library using HiSeq 2000 platforms.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
transcriptomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
RNA-Seq reads were mapped to GRCh37 with Gencode v24lift37 annotation using STAR (v2.5.3)
RNA abundance quantified using raw counts from STAR by setting the GeneCounts parameter to quantMode
MACS2 (version 2.0.10.20131216) was used to call peak on the bam files
Trimmed Means of M-Values (TMM) normalization was performed on the library size adjusted read counts before being converted to FPKM with the Bioconductor package edgeR (v3.12.1)
Genome_build: GRCh37
Supplementary_files_format_and_content: txt file with gene level read counts
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
Feb 08, 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 |
GPL20795 |
| Series (2) |
| GSE113124 |
Widespread and Functional RNA Circularization in Localized Prostate Cancer. |
| GSE123940 |
RNA-seq after KD or OE of circRNAs or linear gene |
|
| Relations |
| BioSample |
SAMN10602551 |
| SRA |
SRX5140808 |
