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Series GSE29218 Query DataSets for GSE29218
Status Public on Jul 01, 2012
Title A draft map of cis-regulatory sequences in the mouse genome [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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 19 tissues and primary cell types were examined.
Contributor(s) Shen Y, Yue F, Ren B
Citation(s) 22763441
Submission date May 11, 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 (122)
GSM722631 RenLab-CTCF-cortex
GSM722632 RenLab-H3K4me1-cortex
GSM722633 RenLab-H3K4me3-cortex
This SubSeries is part of SuperSeries:
GSE29184 A draft map of cis-regulatory sequences in the mouse genome
SRA SRP006786
BioProject PRJNA142963

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Supplementary file Size Download File type/resource
GSE29218_RAW.tar 123.7 Gb (http)(custom) TAR (of BAM, BIGWIG, BOWTIE, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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