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:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

7 related Platforms

15 Samples

Download data: BED

(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:

GPL13802 GPL10999 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:

Homo sapiens; Macaca mulatta; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL13766 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) While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. more...

Organism:

Mus musculus; Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

8 related Platforms

98 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, TXT

(Submitter supplied) DNA methylation in sperm is among the most important factors shaping evolution of the mammalian genome. By directly altering germline mutation rates, the DNA methylation system has shaped the CpG landscape of mammalian genomes, resulting in the CpG island phenomenon. Yet little is known about how this system itself has co-evolved with its substrate during mammalian evolution. We analyzed full-genome single-CpG DNA methylation profiles in sperm from human, chimp, gorilla, rhesus, mouse, rat and dog. more...

Organism:

Gorilla gorilla; Rattus norvegicus; Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL18694 GPL16540 GPL21650

12 Samples

Download data: TXT

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

Organism:

Pan troglodytes; Homo sapiens

Type:

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

Platform:

GPL27803

33 Samples

Download data

(Submitter supplied) Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27803

25 Samples

Download data: TXT

(Submitter supplied) Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27803

8 Samples

Download data: TXT

(Submitter supplied) Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

Organism:

Pongo abelii; Pan troglodytes troglodytes; Pan troglodytes; Gorilla gorilla; Pongo pygmaeus; Pongo sp.; Homo sapiens; Gorilla gorilla gorilla; Pan paniscus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7749

58 Samples

Download data: PAIR, TXT

(Submitter supplied) Gene expression in adult male and female mouse liver was assayed by RNA-seq, as part of a study on chromatin states in male and female mouse and their role in sex-biased liver gene expression (A Sugathan and DJ Waxman (2013) Mol Cell Biol. 33:3594-3610. doi: 10.1128/MCB.00280-13).

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: BED

(Submitter supplied) Here we map six chromatin modifications -- H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K9me3, and H3K27me3 -- genome-wide in male and female mouse liver in order to identify histone modifications that characterize sex-biased genes and sex-biased DNase hypersensitive sites and their regulation by plasma growth hormone (GH) profiles, which are sexually dimorphic. We find distinct mechanisms of regulation in male liver and female liver: sex-dependent K27me3-mediated repression is an important mechanism of repression of female-biased, but not of male-biased, genes, and a sex-dependent K4me1 distribution, suggesting nucleosome repositioning by pioneer factors, is observed at male-biased, but not female-biased, regulatory sites. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL9250

38 Samples

Download data: BED, TXT

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

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

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

6 related Platforms

24 Samples

Download data

(Submitter supplied) Genomic changes acquired in human evolution contribute to the unique abilities of human brain. However, characterizing the molecular underpinnings of human-specific traits is a multifaceted challenge due to the cellular heterogeneity of human brain and complex regulation of gene expression. Here, we performed single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC-seq (snATAC-seq) in human, chimpanzee, and rhesus macaque brain tissue (brodmann area 23, posterior cingulate cortex). more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

6 related Platforms

12 Samples

Download data: MTX, RDS, TXT, XLSX

(Submitter supplied) Genomic changes acquired in human evolution contribute to the unique abilities of human brain. However, characterizing the molecular underpinnings of human-specific traits is a multifaceted challenge due to the cellular heterogeneity of human brain and complex regulation of gene expression. Here, we performed single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC-seq (snATAC-seq) in human, chimpanzee, and rhesus macaque brain tissue (brodmann area 23, posterior cingulate cortex). more...

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

12 Samples

Download data: MTX, RDS, TXT, XLSX

(Submitter supplied) DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. more...

Organism:

Gorilla gorilla gorilla; Pongo abelii; Gorilla beringei graueri; Pan paniscus; Pan troglodytes schweinfurthii; Pan troglodytes troglodytes; Pongo pygmaeus; Homo sapiens; Pan troglodytes verus

Type:

Methylation profiling by array

Platform:

GPL13534

32 Samples

Download data: TXT

(Submitter supplied) Variation in gene regulation is thought to have played an important role in the evolution of primates, and many studies have documented differences in mRNA expression levels across primate species. However, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are more directly tied to phenotypic differences. To address this question, we used high-resolution, quantitative mass spectrometry to collect thousands of protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines (LCLs). more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16809 GPL11154 GPL14954

16 Samples

Download data: TXT

(Submitter supplied) Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. more...

Organism:

Pan troglodytes; Rattus norvegicus; Macaca mulatta; Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

8 related Platforms

24 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. These files are part of a larger study where we establish that pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is a novel mechanism for establishing widespread sex differences in chromatin accessibility and transcription factor binding, which are closely linked to sex-biased gene expression and the sexual dimorphism of liver function. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

35 Samples

Download data

(Submitter supplied) Sequencing files provided here are mouse liver DNase-seq to identify DNase hypersensitive sites (DHS) in livers from intact and hypox female, hypox male, and hypox male mice given a single injection of GH and then euthanized 30, 90, or 240 minutes later. This is part of a larger study that includes DNase-seq in mouse liver from intact males determined to be STAT5-high or STAT5-low based on an endogenous pulse of GH/STAT5. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

14 Samples

Download data: XLSX