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Sample GSM1545085 Query DataSets for GSM1545085
Status Public on Nov 15, 2014
Title GT17
Sample type SRA
 
Source name Gastric cancer, stomach
Organism Homo sapiens
Characteristics tissue type: gastric cancer tumor
class: IIIA
location: Proximal
Extracted molecule total RNA
Extraction protocol RNA isolation, library preparation (paired-end, 50nt and 35nt), template bead preparation and SOLiD v 4.0 sequencing followed standard protocols provided by Life Technologies (Carlsbad, California, USA)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD 4 System
 
Data processing The raw reads were aligned to the human genome (hg19) using SOLiD BioScope (version 1.3) whole transcriptome analysis protocol with default parameters and the alignments with properly-paired reads were saved in BAM format for further analysis.
The read counts per gene were calculated using R packages, Rsamtools (1.10.2) and GenomicFeatures (1.12.1).
The read counts were normalized to scale the raw library sizes using the weighted trimmed mean of M-values implemented in R package, edgeR (3.0.8).
If the number of overlapped read of any given gene is less than one per million total mapped read for 95% of the samples, this gene was excluded from further analysis.
A negative binomial generalized linear model was fit to each gene expression and the Wald test was performed to identify differentially expressed genes. The Benjamini-Hochberg method was used to control false discovery rate (FDR). These calculations were performed in R (2.15.1) using edgeR (3.0.8).
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is a data matrix saved in ASCII format. The rows are genes and columns are samples. Each entry is count per million, which is normalized read count per gene per sample divided by library size and multiplying by one million.
 
Submission date Nov 14, 2014
Last update date May 15, 2019
Contact name Han Liang
E-mail(s) hliang1@mdanderson.org
Phone 1713-945-9815
Organization name The University of Texas MD Anderson Cancer Cencer
Department Bioinformatics and Computational Biology
Street address 1400 Pressler Street
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL13393
Series (1)
GSE63288 HNF4α is a therapeutic target that links AMPK to WNT signaling in early-stage gastric cancer
Relations
BioSample SAMN03195584
SRA SRX759675

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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