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Series GSE63648 Query DataSets for GSE63648
Status Public on Mar 06, 2015
Title Evolutionary changes in promoter and enhancer activity during human corticogenesis (human)
Organism Homo sapiens
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 in humans. However, the lack of a regulatory map of the human 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 human, rhesus, and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in human 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 human cortex. We identified multiple modules enriched in human 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 human cortical evolution.
Overall design For Human and Mouse samples, two biological replicates from four cortical tissue stages, each stage with separate H3K27ac and H3K4me2 ChIPs as well as an input control. Identical ChIPs for two replicates at two stages in Rhesus cortex, and one rhesus stage without replication.
Contributor(s) Reilly SK, Noonan JP
Citation(s) 25745175
Submission date Nov 25, 2014
Last update date Mar 27, 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 (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (24)
GSM1554660 Hu_7pcw_H3K27ac_rep1
GSM1554661 Hu_7pcw_H3K27ac_rep2
GSM1554662 Hu_7pcw_H3K4me2_rep1
This SubSeries is part of SuperSeries:
GSE63649 Evolutionary changes in promoter and enhancer activity during human corticogenesis
BioProject PRJNA268529

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Supplementary file Size Download File type/resource
GSE63648_12Fpcw_ac_Hu_gain.bed.gz 9.5 Kb (ftp)(http) BED
GSE63648_12Fpcw_me2_Hu_gain.bed.gz 21.2 Kb (ftp)(http) BED
GSE63648_12Opcw_ac_Hu_gain.bed.gz 13.2 Kb (ftp)(http) BED
GSE63648_12Opcw_me2_Hu_gain.bed.gz 34.0 Kb (ftp)(http) BED
GSE63648_7pcw_ac_Hu_gain.bed.gz 24.3 Kb (ftp)(http) BED
GSE63648_7pcw_me2_Hu_gain.bed.gz 50.0 Kb (ftp)(http) BED
GSE63648_8_5pcw_ac_Hu_gain.bed.gz 18.3 Kb (ftp)(http) BED
GSE63648_8_5pcw_me2_Hu_gain.bed.gz 32.8 Kb (ftp)(http) BED
GSE63648_RAW.tar 43.9 Gb (http)(custom) TAR (of BED, BW)
GSE63648_ReadMe_Bed_files_contents.txt 260 b (ftp)(http) TXT
Raw data not provided for this record
Processed data provided as supplementary file

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