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Sample GSM1538083 Query DataSets for GSM1538083
Status Public on Jun 09, 2017
Title MC6
Sample type SRA
 
Source name omental metastasis
Organism Homo sapiens
Characteristics patient id: 11
patient age at resection: 16.6
patient sex: F
Extracted molecule total RNA
Extraction protocol RNA was extracted from fresh frozen tissue using the Roche High Pure FFPE kit (Roche Diagnostics). After Ribogreen quantification and quality control via Agilent BioAnalyzer, 0.5 to 1 ug of total RNA underwent stranded TruSeq library preparation according to the manufacturer's instructions (Illumina), with 6 cycles of PCR.
Samples were barcoded and run on a HiSeq 2000 in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina). An average of 69 million paired reads were generated per sample. Ribosomal reads represented at most 0.83% of total reads, while mRNA bases accounted for an average of 61% of reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sample_02998_MC6
Data processing Base calls were made using HiSeq Control Software v.2.0.10.0
Spliced mapping was run with TopHat2 (Bowtie2) to the hg19 genome using the RefSeq gene models from UCSC.
Expression levels were then computed using HTSeq.
Raw expression levels were normalized using Bioconductor package DESeq.
Genome_build: hg19
Supplementary_files_format_and_content: contains HTSeq counts that have been scaled(normalized) using Bioconductor package DESeq
 
Submission date Nov 05, 2014
Last update date May 15, 2019
Contact name Bic MSKCC
Organization name Memorial SLoan-Kettering Cancer Center
Street address 1275 York Ave.
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL16791
Series (1)
GSE63018 Genome and transcriptome profiling of fibrolamellar carcinoma [RNA-Seq]
Relations
BioSample SAMN03165767
SRA SRX752933

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

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