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Series GSE42237 Query DataSets for GSE42237
Status Public on May 22, 2013
Title The genomic landscape of cohesin-associated chromatin interactions
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Cohesin is implicated in establishing tissue-specific DNA loops that target enhancers to promoters, and also localizes to sites bound by the insulator protein CTCF, which blocks enhancer-promoter communication. However, cohesin-associated interactions have not been characterized on a genome-wide scale. Here we performed chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) of the cohesin subunit SMC1A in developing mouse limb. We identified 2,264 SMC1A interactions, of which 1,491 (65%) involved sites co-occupied by CTCF. SMC1A participates in tissue- specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output. In contrast to previous studies, we also identified interactions between promoters and distal sites that are maintained in multiple tissues, but are poised in embryonic stem cells and resolve to tissue-specific activated or repressed chromatin states in the mouse embryo. Our results reveal the diversity of cohesin- associated interactions in the genome and highlight their role in establishing the regulatory architecture of development.
Overall design Smc1a ChIA-PET, RNA-seq, chromatin state maps (H3K27ac, H3K27me3, H3K4m2), and CTCF and Smc1a binding in mouse embryonic limb bud (E11.5)
Contributor(s) DeMare LE, Noonan JP
Citation(s) 23704192
Submission date Nov 13, 2012
Last update date May 15, 2019
Contact name Laura DeMare
Organization name Yale University School of Medicine
Department Genetics
Lab James Noonan
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (26)
GSM1036113 Input_CTCF_e11.5limb
GSM1036114 Input_H3K4me2_e11.5limb
GSM1036115 Input_H3K27me3_Smc1rep2_e11.5limb
BioProject PRJNA179381
SRA SRP017162

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Supplementary file Size Download File type/resource
GSE42237_RAW.tar 8.3 Gb (http)(custom) TAR (of BED, BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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