|
| Status |
Public on Aug 22, 2017 |
| Title |
786-O VHL RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
ccRCC cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: wildtype VHL restoration
source: 786-O (ATCC CRL1932)
|
| Treatment protocol |
786-O cells stably expressing RC3 empty vector (EV) or wildtype VHL (VHL) were kindly provided by Dr. Michael Ohh (University of Toronto). 786-O cells were also treated with either non-targeting control or pooled siRNA against HIF2a (Dharmacon).
|
| Growth protocol |
786-O cells were grown in RPMI-1640 medium (Sigma) supplemented with 10% fetal bovine serum (Gibco). Cells were maintained in a 5% CO2-humidified incubator at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy Mini kit.
RNAseq libraries were prepared using Illumina Tru-Seq RNA Sample Preparation v2 protocol, according to the manufacturer’s instructions. Briefly, poly-A RNAs were recovered from 1 µg of input total RNA using poly-T oligo conjugated magnetic beads. The recovered poly-A RNA was chemically fragmented and converted to SuperScript II and random primers. The second strand was synthesized using the Second Strand Master Mix. Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), diluted to 11 pM and applied to an Illumina flow cell using the Illumina Cluster Station.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the human genome (hg19) using TopHat2-2.0.12 [5] (default parameter and --library-type fr-firststrand) and only uniquely mapped reads were analysed.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files generated from uniquely mapped reads
|
| |
|
| Submission date |
Jul 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaosai Yao |
| E-mail(s) |
xiaosai.yao@gmail.com, yao.xiaosai@gene.com
|
| Phone |
+65 68088271
|
| Organization name |
Genome Institute of Singapore
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE86095 |
VHL deficiency drives enhancer activation of oncogenes in clear cell renal cell carcinoma |
| GSE102097 |
VHL/HIF2a axis alters transcriptomic profiles in ccRCC |
|
| Relations |
| BioSample |
SAMN07428909 |
| SRA |
SRX3051175 |
