|
| Status |
Public on Aug 22, 2017 |
| Title |
77972083T ccRCC RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
ccRCC tumor
|
| Organism |
Homo sapiens |
| Characteristics |
individual: patient 77972083
disease state: ccRCC
tissue: ccRCC tumor
|
| 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 |
| GSE102101 |
Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs |
|
| Relations |
| BioSample |
SAMN07429591 |
| SRA |
SRX3051321 |
