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Status |
Public on Nov 15, 2014 |
Title |
GT2 |
Sample type |
SRA |
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Source name |
Gastric cancer, stomach
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Organism |
Homo sapiens |
Characteristics |
tissue type: gastric cancer tumor class: IB location: Distal
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
AB SOLiD 4 System |
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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.
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Submission date |
Nov 14, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Han Liang |
E-mail(s) |
hliang1@mdanderson.org
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Phone |
1713-945-9815
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Organization name |
The University of Texas MD Anderson Cancer Cencer
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Department |
Bioinformatics and Computational Biology
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Street address |
1400 Pressler Street
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platform ID |
GPL13393 |
Series (1) |
GSE63288 |
HNF4α is a therapeutic target that links AMPK to WNT signaling in early-stage gastric cancer |
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Relations |
BioSample |
SAMN03195608 |
SRA |
SRX759660 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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