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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| Overall design |
Cortex Hi-C experiment were conducted in biological replicates
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| 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 |
| E-mail(s) |
biren@ucsd.edu
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| Organization name |
University of California, San Diego
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE29184 |
A draft map of cis-regulatory sequences in the mouse genome |
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| Relations |
| SRA |
SRP009996 |
| BioProject |
PRJNA150507 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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