|
| Status |
Public on Mar 08, 2016 |
| Title |
Pt 392 |
| Sample type |
SRA |
| |
|
| Source name |
clear cell RCC tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
diagnosis: Renal cell carcinoma
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were homogenized in Trizol and processed according to instructions with reagent.
Follow Ion Torrent protocol, start with 100ng RNA using Ambion Low Input RiboMinus Eukaryote System v2 kit + LifeTech Ion Total RNA seq kit V2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Raw output BAMs were converted back to FASTQ using PICARD Sam2Fastq. Reads were then mapped to the human genome using rnaStar. The genome used was HG19 with junctions from ENSEMBL (GRCh37.69_ENSEMBL) and a read overhang of 49. Gene level counts were computed using htseq-count and the same gene models as used in the mapping step.
HTSeq v0.5.4 is used for feature counting.
Counts were normalized and rescaled into log2 counts using the limma R package
Genome_build: hg19
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment
|
| |
|
| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Zhao |
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Genomics Core
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE74734 |
An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma |
|
| Relations |
| BioSample |
SAMN04246342 |
| SRA |
SRX1422032 |
