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) Using reduced representation bisulfite sequencing (RRBS), we have compared the methylomes of neuronal and non-neuronal cells from three female human and three chimpanzee cortices (Brodmann area 10). Differentially methylated regions (DMRs) with genome-wide significance were enriched in specific chromosomal regions. Intraspecific methylation differences between neuronal and non-neuronal cells were approximately three times more abundant than interspecific methylation differences between human and chimpanzee cell types. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9115 GPL9378

12 Samples

Download data: CSV

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

Organism:

Macaca fuscata; Pan troglodytes; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9115 GPL19621 GPL9378

5 Samples

Download data: TXT

(Submitter supplied) It has been thought that epigenetic changes underlie the evolutionary divergence of phenotype between closely related species. To study differences in DNA methylation between humans and chimanzees, we collected methylated DNAs from age- and gender-matched PBL samples of the two species, and deeply sequenced. The map counts were then converted to MEDIPS scores in 100-bp bins, which are related to absolute methylation levels.

Organism:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9115 GPL9378

4 Samples

Download data: TXT

(Submitter supplied) Next Generation Sequencing of Unmethylated Alu (NSUMA) interrogation of more than 130,000 individual Alus for differential methylation with concomitant analysis of copy number variations applied to the study of hypomethylation in primates.

Organism:

Pan troglodytes; Pongo pygmaeus; Gorilla gorilla; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

6 related Platforms

14 Samples

Download data: TXT

(Submitter supplied) Changes in gene regulation level have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels yet we know much less about the extent to which regulatory mechanisms differ between species. To begin addressing this gap, we performed a comparative epigenetic study in primate lymphoblastoid cell lines (LCLs), to query the contribution of RNA polymerase II (Pol II) and four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) to inter-species variation in gene expression levels. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

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

5 related Platforms

98 Samples

Download data: BED

(Submitter supplied) DNA methylation is critical for development and is strongly associated with gene regulation. Variation in the DNA methylome between closely related species may reveal unique functional adaptation. We have implemented a novel inter-primate DNA methylation genome-wide analysis between human, chimpanzee and rhesus macaque to identify human species-specific Differentially Methylated Regions (human s-DMRs) in orthologous loci. more...

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9378 GPL9160 GPL9115

3 Samples

Download data: BED, BW

(Submitter supplied) we used RNA-Seq to quantify the RNA editing level at more than 8,000 previously annotated exonic A-to-I RNA editing sites in two brain regions - prefrontal cortex and cerebellum - of humans, chimpanzees and rhesus macaques. We observed substantial conservation of RNA editing levels between the brain regions, as well as among the three primate species. Evolutionary changes in RNA editing were nonetheless evident among the species. more...

Organism:

Macaca mulatta; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9160 GPL9378

8 Samples

Download data: TXT

(Submitter supplied) We have quantified gene expression in five tissues (brain, heart, kidney, liver and testis) from humans, chimpanzees and rhesus macaques using the Illumina NlaIII Digital Gene Expression (DGE) protocol. This dataset extends a previous microarray study by Khaitovich et al. (Khaitovich et al. 2005) with the rhesus macaque outgroup and complements other previously generated tissue transcriptome profiles from primates (Enard et al. more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

6 related Platforms

71 Samples

Download data: TSV

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

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

5 related Platforms

92 Samples

Download data: CEL, TXT

(Submitter supplied) We identified human-specific gene expression patterns in the brain by comparing expression with chimpanzee and rhesus macaque.

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115 GPL9160

44 Samples

Download data: TXT

(Submitter supplied) Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.

Organism:

Macaca mulatta; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9160 GPL9378

12 Samples

Download data: TXT

(Submitter supplied) Among other factors, changes in gene expression on the human evolutionary lineage have been suggested to play an important role in the establishment of human-specific phenotypes. However, the molecular mechanisms underlying these expression changes are largely unknown. Here, we have explored the role of microRNA (miRNA) in the regulation of gene expression divergence between adult humans, chimpanzees and rhesus macaques, in two brain regions: prefrontal cortex and cerebellum. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by array; Non-coding RNA profiling by array; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

46 Samples

Download data: CEL, TXT

(Submitter supplied) During germ cell and preimplantation development, mammalian cells undergo nearly complete reprogramming of DNA methylation patterns. We profiled the methylomes of human and chimp sperm as a basis for comparison to methylation patterns of ES cells. While the majority of promoters escape methylation in both ES cells and sperm, the corresponding hypomethylated regions show substantial structural differences. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115

4 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Changes in gene regulation are thought to play an important role in speciation and adaptation, especially in primates. However, we still know relatively little about the mechanisms underlying regulatory evolution. In particular, the extent to which epigenetic modifications underlie gene expression differences between primates is not yet known. Our study focuses on an epigenetic histone modification, H3K4me3, which is thought to promote transcription. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

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

Platforms:

GPL9115 GPL9160 GPL9378

21 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

Platforms:

GPL9115 GPL9378

149 Samples

Download data: BED, TXT

(Submitter supplied) We examined genome-wide variation in transcription factor binding in different individuals and a chimpanzee using chromatin immunoprecipitation followed by massively-parallel sequencing (ChIP-Seq). The binding sites of RNA Polymerase II (Pol II) as well as a key regulator of immune responses, NFkB, were mapped in ten HapMap lymphoblastoid cell lines derived from individuals of African, European, and Asian ancestry, including a parent-offspring trio. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9378 GPL9115

67 Samples

Download data: BED, TXT

(Submitter supplied) Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9160 GPL9115 GPL9378

36 Samples

Download data: TXT