GEO DataSets

(Submitter supplied) Evolution of transcriptional regulation is thought to be a major cause of the evolution of phenotypic traits. We compared DNase I Hypersensitive sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and macaque). We identified approximately 90,000 DHS sites, of which 59% are not significantly different between species, 27% are differential and likely due to a single evolutionary change, and 14% are differential and likely due to multiple changes. more...

Organism:

Gorilla gorilla; Pongo pygmaeus; Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

15 Samples

Download data: BED

(Submitter supplied) Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes.

Organism:

Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

4 related Platforms

64 Samples

Download data: TXT, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL13802 GPL13766

30 Samples

Download data: BIGWIG

(Submitter supplied) The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expressed between species, but the regulatory elements contributing to these differences are largely unknown. Here we report a genome-wide comparison of active gene regulatory elements in human, chimpanzee, and macaque, and we identify hundreds of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence. These elements contain evidence of natural selection and correlate with species-specific changes in gene expression. Polymorphic DNA bases in transcription factor motifs that we found in these regulatory elements may be responsible for the varied biological functions across species. This study directly links phenotypic and transcriptional differences between species with changes in chromatin structure.

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13766 GPL10999 GPL13802

15 Samples

Download data: BIGWIG

(Submitter supplied) The human genome shares a remarkable amount of genomic sequence with our closest living primate relatives. Researchers have long sought to understand what regions of the genome are responsible for unique species-specific traits. Previous studies have shown that many genes are differentially expressed between species, but the regulatory elements contributing to these differences are largely unknown. Here we report a genome-wide comparison of active gene regulatory elements in human, chimpanzee, and macaque, and we identify hundreds of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence. These elements contain evidence of natural selection and correlate with species-specific changes in gene expression. Polymorphic DNA bases in transcription factor motifs that we found in these regulatory elements may be responsible for the varied biological functions across species. This study directly links phenotypic and transcriptional differences between species with changes in chromatin structure.

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL13802 GPL13766

15 Samples

Download data: TXT

(Submitter supplied) Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. more...

Organism:

Gorilla gorilla; Homo sapiens; Mus musculus; Monodelphis domestica; Pan troglodytes; Pongo pygmaeus; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus

Type:

Expression profiling by high throughput sequencing

10 related Platforms

131 Samples

Download data