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Series GSE42413 Query DataSets for GSE42413
Status Public on Jul 02, 2013
Title The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
Organisms Macaca mulatta; Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find that 13% of promoters and 11% of enhancers have gained activity on the human lineage since the human-rhesus divergence. These gains largely arose by modification of ancestral regulatory activities in the limb or potential co-option from other tissues and are likely to have heterogeneous genetic causes. Most enhancers that exhibit gain of activity in humans originated in mammals. Gains at promoters and enhancers in the human limb are associated with increased gene expression, suggesting they include molecular drivers of human morphological evolution.
Overall design ChIP-Seq and RNA-Seq of autopod tissue of developing limb buds of Human (E33-E47), rhesus (E31-E36), and mouse (E10.5-E13.5).

No raw data are provided for human samples. Human alignments were anonymized by removing sequence information and converting to bed format.
Contributor(s) Cotney J, Noonan JP
Citation(s) 23827682
Submission date Nov 20, 2012
Last update date May 15, 2019
Contact name Justin Cotney
Organization name UConn Health
Department Genetics and Genome Sciences
Lab Cotney Lab
Street address 400 Farmington Ave.
City Farmington
State/province CT
ZIP/Postal code 06030-6403
Country USA
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL14954 Illumina HiSeq 2000 (Macaca mulatta)
Samples (56)
GSM1039522 human_E33_rep1_input
GSM1039523 human_E33_rep2_input
GSM1039524 human_E41_rep1_input
BioProject PRJNA181397
SRA SRP017259

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE42413_RAW.tar 67.9 Gb (http)(custom) TAR (of BAM, BED, BW)
GSE42413_e10.5_3_h3k27acEnrichedRegions0.00001.bed.gz 620.8 Kb (ftp)(http) BED 5.3 Gb (ftp)(http) BW
GSE42413_e11.5_2_h3k27acEnrichedRegions0.00001.bed.gz 379.6 Kb (ftp)(http) BED 5.5 Gb (ftp)(http) BW
GSE42413_e12.5_1_h3k27acEnrichedRegions0.00001.bed.gz 466.9 Kb (ftp)(http) BED 5.2 Gb (ftp)(http) BW
GSE42413_e12.5_2_h3k27acEnrichedRegions0.00001.bed.gz 566.1 Kb (ftp)(http) BED 5.5 Gb (ftp)(http) BW
GSE42413_e13.5_1_h3k27acEnrichedRegions0.00001.bed.gz 301.8 Kb (ftp)(http) BED 5.3 Gb (ftp)(http) BW
GSE42413_e13.5_2_h3k27acEnrichedRegions0.00001.bed.gz 276.7 Kb (ftp)(http) BED 4.9 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data not provided for this record
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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