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Series GSE29184 Query DataSets for GSE29184
Status Public on Jul 01, 2012
Title A draft map of cis-regulatory sequences in the mouse genome
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Genome variation profiling by high throughput sequencing
Summary The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 billion bases of the mouse genome share a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. To date, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but it alone cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including human, D. melanogaster and C. elegans. We have applied the same experimental approach to a diverse set of 19 tissues and cell types in the mouse, producing a map of nearly 300,000 murine cis-regulatory sequences. This map provides functional annotation to nearly 11% of the mouse genome, and over 70% of conserved, non-coding sequences (CNS). We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and study of mechanisms regulating tissue-specific gene expression.

This SuperSeries is composed of the SubSeries listed below.
Overall design 19 tissues and primary cell types were examined using ChIP-Seq, RNA-Seq. Additionally we performed HiC experiments in mouse cortex.
Contributor(s) Shen Y, Yue F, Ren B
Citation(s) 22763441
Submission date May 10, 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 (3)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (143)
GSM722631 RenLab-CTCF-cortex
GSM722632 RenLab-H3K4me1-cortex
GSM722633 RenLab-H3K4me3-cortex
This SuperSeries is composed of the following SubSeries:
GSE29218 A draft map of cis-regulatory sequences in the mouse genome [ChIP-Seq]
GSE29278 A draft map of cis-regulatory sequences in the mouse genome [RNA-Seq]
GSE34587 A draft map of cis-regulatory sequences in the mouse genome [HiC]
BioProject PRJNA139991

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
GSE29184_RAW.tar 149.0 Gb (http)(custom) TAR (of BAM, BIGWIG, BOWTIE, TXT)
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