GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE34587 Query DataSets for GSE34587
Status Public on Jul 01, 2012
Title A draft map of cis-regulatory sequences in the mouse genome [HiC]
Organism Mus musculus
Experiment type Other
Summary As the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression.
Overall design Cortex Hi-C experiment were conducted in biological replicates
Contributor(s) Shen Y, Yue F, Ren B
Citation(s) 22763441
Submission date Dec 20, 2011
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (2)
GSM938750 RenLab-HiC-cortex_replicate one
GSM938751 RenLab-HiC-cortex_replicate two
This SubSeries is part of SuperSeries:
GSE29184 A draft map of cis-regulatory sequences in the mouse genome
SRA SRP009996
BioProject PRJNA150507

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
GSE34587_GSM938750_cortex_HindIII_ori_HiC.nodup.hic.summary.txt.gz 6.4 Gb (ftp)(http) TXT
GSE34587_GSM938751_cortex_HindIII_replicate_Hic.nodup.hic.summary.txt.gz 5.1 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap