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Series GSE80793 Query DataSets for GSE80793
Status Public on Feb 15, 2018
Title CpG island mediated linear and spatial gene partitioning (RNA-seq)
Sample organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. 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 RNA-seq gene expression analyses 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 PRJNA319992

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE80793_human_RNA-seq_profile.txt.gz 1.0 Mb (ftp)(http) TXT
GSE80793_mouse_RNA-seq_profile.txt.gz 2.6 Mb (ftp)(http) TXT
Processed data are available on Series record

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