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Series GSE80797 Query DataSets for GSE80797
Status Public on Feb 15, 2018
Title CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)
Sample organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary In order to test the global effects of CpG island-centered gene regulation on global gene expression profile, pA+ RNA-seq data of diverse tissues and cell lines were gathered and profiled. All available mouse poly-A positive RNA-seq data (3,818 samples) were summarized and downloaded at May, 5th, 2015. Among them, excluding single cell RNA-seq or experiments whose expression verified gene counts are small (less than 5,000 genes with RPKM 0.5 or higher), 1,524 high quality RNA-seq data were used. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsk├Âld et al., 2009).
 
Overall design pA+ RNA-seq gene expression analysis in diverse mouse and human samples.
 
Contributor(s) Kim J, Beck S
Citation(s) 29529258
Submission date Apr 28, 2016
Last update date May 17, 2018
Contact name Jonghwan Kim
E-mail(s) jybella@utexas.edu
Phone 512-232-8046
Organization name University of Texas at Austin
Department Department of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology
Lab Kim Lab
Street address 2506 Speedway NMS 4.246
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
This SubSeries is part of SuperSeries:
GSE80799 Implications of CpG islands on chromosomal architectures and modes of global gene regulation
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BioProject PRJNA319996

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GSE80797_combined_mouse_pA+RNA-seq_profile.txt.gz 160.3 Mb (ftp)(http) TXT
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