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Series GSE37151 Query DataSets for GSE37151
Status Public on Apr 16, 2014
Title Expanding the Catalog of Enhancer Marks In Vivo
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary While the majority of protein-coding genes in the human genome have been identified, the location of the regulatory sequences that control their expression in time and space remains poorly defined. The importance of identifying these elements is underscored by a growing number of studies (such as GWAS) supporting a relationship between variation in non-coding sequences and human disease. We previously demonstrated that ChIP-Seq with p300 directly on human or mouse tissues represents a powerful method to identify the location and tissue-specific activity pattern of enhancers in the genome. While p300 is a highly specific chromatin mark for the prediction of in vivo enhancers, it is not without limitations. In particular, comparison of p300-bound regions with previously generated enhancer sets shows that the majority of enhancers are activated independently of p300. To attempt to identify a larger proportion of enhancers in vivo, we have focused on several additional transcriptional coactivators that are hypothesized to be associated with active tissue-specific enhancers. To overcome the limited availability of ChIP-seq grade antibodies for these coactivators, FLAG-tag knock-in mice were generated and ChIP-seq using a FLAG antibody was performed on various tissues from e11.5 mouse embryos. Indeed, as these mouse lines have become available we have validated their valuable role as marks for transcriptional enhancers in vivo. These ongoing studies are expected to further expand the catalogue of in vivo functional enhancers, which will aid in the decoding of the regulatory genome and provide new insights into the role of gene regulation in human biology and disease. In addition to FLAG data, this accession includes histone acetylation / methylation ChIP-seq data from e11.5 mouse embryonic tissues. Histone ChIP-seq data was used in combination with FLAG data for various computational analyses.
Overall design Examination of FLAG-labeled transcriptional coactivator binding in mouse embryonic stage 11.5 and embryonic stem cells.
Contributor(s) Blow MJ, Nord AS, Pennacchio LA, Attanasio C
Citation(s) 24752179
Submission date Apr 10, 2012
Last update date May 15, 2019
Contact name Matthew James Blow
Phone 510-486-6590
Fax 510-486-7004
Organization name Lawrence Berkeley National Laboratory
Department Genomics Division
Lab Rubin / Pennacchio
Street address 1 Cyclotron Road
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (34)
GSM912546 mouse_e11.5_face_smarca4-flag
GSM912547 mouse_e11.5_forebrain_smarca4-flag
GSM912548 mouse_e11.5_forebrain_control
BioProject PRJNA158429
SRA SRP012148

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Supplementary file Size Download File type/resource
GSE37151_RAW.tar 5.9 Gb (http)(custom) TAR (of BED, TXT, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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