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Sample GSM1931344 Query DataSets for GSM1931344
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
BioSample SAMN04246342
SRA SRX1422032

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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