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Series GSE60838 Query DataSets for GSE60838
Status Public on Mar 06, 2015
Title Evolutionary changes in promoter and enhancer activity during corticogenesis (non-human)
Organisms Macaca mulatta; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Evolutionary changes in gene regulation during cortical development likely contributed to the expansion and specialization of the cortex. However, the lack of a regulatory map of the embryonic cortex has hindered identification of these changes and the biological processes they influenced. We performed genome-wide epigenetic profiling to compare promoter and enhancer activity during corticogenesis in rhesus and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in based on increased epigenetic marking. To detect biological pathways enriched for these changes, we mapped promoters and enhancers exhibiting epigenetic gains onto modules of co-expressed genes constructed using spatio-temporally rich expression data from developing cortex. We identified multiple modules enriched in lineage epigenetic gains. Gains in enriched modules were associated with genes functioning in neuronal proliferation and migration, cortical patterning, and the extracellular matrix. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes in corticogenesis, providing insight into cortical evolution.
Overall design For mouse samples, two biological replicates each from four cortical tissues (embryonic day 11.5 (E11.5), E14.5, E17.5 frontal, and E17.5 occipital. For Rhesus, two biological replicates each from 12 p.c.w. frontal and 12 p.c.w. occipital and one replicate from 8 p.c.w. Each replicate is comprised of H3K27ac and H3K4me2 ChIPs in addition to a shared input control.
Contributor(s) Reilly SK, Noonan JP
Citation(s) 25745175
Submission date Aug 27, 2014
Last update date May 15, 2019
Contact name Steven K Reilly
Organization name Yale University
Department Genetics
Lab Noonan
Street address 333 Cedar St
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
Samples (39)
GSM1489701 Mm_e11_H3K27ac_rep1
GSM1489702 Mm_e11_H3K27ac_rep2
GSM1489703 Mm_e11_H3K4me2_rep1
This SubSeries is part of SuperSeries:
GSE63649 Evolutionary changes in promoter and enhancer activity during human corticogenesis
BioProject PRJNA259649
SRA SRP045830

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Supplementary file Size Download File type/resource
GSE60838_RAW.tar 68.6 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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