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Series GSE141563 Query DataSets for GSE141563
Status Public on May 15, 2020
Title Novel enhancer emerge with high interindividual variability and less frequently associate with disease
Organism Callithrix jacchus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Mutations in non-coding regulatory DNA such as enhancers underlie a wide variety of diseases including developmental disorders and cancer. As enhancers rapidly evolve, understanding their function and configuration in non-human disease models can have important clinical applications. Here, we analyze enhancer configurations in tissues isolated from the common marmoset, a widely used primate model for human disease. Integrating these data with human and mouse data, we find that enhancers containing trait-associated variants are preferentially conserved. In contrast, most human-specific enhancers are highly variable between individuals, with a subset failing to contact promoters. These are located further away from genes and more often reside in inactive B-compartments. Our data show that enhancers typically emerge as instable elements with minimal biological impact prior to their integration in a transcriptional program. Furthermore, our data provide insight into which trait variations in enhancers can be faithfully modeled using the common marmoset.
Overall design ChIP-sequencing for H3K27ac and H3K4me3 of marmoset tissue samples
Contributor(s) Castelijns B, Baak M, Geeven G, Vermunt MW, Wiggers CR, Timpanaro IS, Kondova I, de Laat W, Creyghton MP
Citation(s) 32579926
Submission date Dec 06, 2019
Last update date Aug 25, 2020
Contact name Menno P Creyghton
Organization name Hubrecht Institute
Lab Creyghton
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platforms (2)
GPL17712 Illumina HiSeq 2000 (Callithrix jacchus)
GPL26636 Illumina NextSeq 500 (Callithrix jacchus)
Samples (39)
GSM4207030 Marmoset_Colon_H3K27ac_1
GSM4207031 Marmoset_Colon_H3K27ac_2
GSM4207032 Marmoset_Colon_H3K4me3_1
BioProject PRJNA593966
SRA SRP234929

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE141563_RAW.tar 4.8 Gb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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