GEO DataSets

Comparison of various human and chimpanzee brain regions. Results provide insight into the genetic basis of human specializations in brain organization and cognition.

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by array, count, 2 species, 12 tissue sets

Platform:

GPL8300

Series:

GSE7540

37 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) The origin of humans was accompanied by the emergence of new behavioral and cognitive functions, including language and specialized forms of abstract representation. However, the molecular foundations of these human capabilities are poorly understood. Because of the extensive similarity between human and chimpanzee DNA sequences, it has been suggested that many of the key phenotypic differences between species result primarily from alterations in the regulation of genes rather than in their sequences. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2678

Platform:

GPL8300

37 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) Comparing different primates to Human; treated vs.untreated Keywords: other

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes; Pongo pygmaeus

Type:

Expression profiling by array

Platform:

GPL1714

80 Samples

Download data

(Submitter supplied) In order to assess the impact of three rounds of linear amplification on the technical reproducibility of gene expression measurements, we performed twelve microarray experiments. We analysed mouse RNA from cortex, cerebellum and liver from one individual. One RNA sample of 5µg from each of the three different tissues was processed according to the standard Affymetrix protocol and hybridized onto mouse gene expression arrays MG_U74Av2. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL81

12 Samples

Download data: CEL

(Submitter supplied) Neurons and endothelial cells were identified by immunohistochemistry in human brains, isolated by laser-capture-microdissection and used to find genes preferentially expressed in the two cell types. Keywords: cell type comparison

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL570 GPL81

25 Samples

Download data: CEL

(Submitter supplied) Comparison of expression in liver samples of human, chimp, orang and rhesus, by using a novel multi-species cDNA array Keywords: other

Organism:

Pan troglodytes; Pongo pygmaeus; Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1714

16 Samples

Download data

(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) 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:

Pan troglodytes; Macaca mulatta; Homo sapiens

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) 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:

Macaca mulatta; Homo sapiens; Pan troglodytes; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

8 related Platforms

98 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, TXT

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

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL8444 GPL5175

15 Samples

Download data: CEL

(Submitter supplied) Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL8444

9 Samples

Download data: CEL

(Submitter supplied) Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

6 Samples

Download data: CEL

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

Organism:

Macaca mulatta; Pan troglodytes

Type:

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

Platforms:

GPL19129 GPL19148

46 Samples

Download data: BW

(Submitter supplied) The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type–specific regulatory landscapes in the cortex re- main largely unexplored. Here we report epigenomic and tran- scriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. more...

Organism:

Pan troglodytes; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19148 GPL19129

14 Samples

Download data: TXT, XLSX

(Submitter supplied) The human cerebral cortex contains many cell types that likely underwent independent functional changes during evolution. However, cell-type–specific regulatory landscapes in the cortex re- main largely unexplored. Here we report epigenomic and tran- scriptomic analyses of the two main cortical neuronal subtypes, glutamatergic projection neurons and GABAergic interneurons, in human, chimpanzee, and rhesus macaque. more...

Organism:

Macaca mulatta; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19129 GPL19148

32 Samples

Download data: BW, XLSX

(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:

Homo sapiens; Pan troglodytes; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9378 GPL9160 GPL9115

36 Samples

Download data: TXT

(Submitter supplied) RNA-Seq technology was widely used to study gene expression, splicing structure and RNA editing. To facilitate transcriptome study in rhesus macaque, and provide an evolutionary context to understand human biology, we performed 90bp × 2, paired-end, strand-specific, polyA-postive RNA-Seq in 10 tissues of the same macaque animals. The data were deposited under accession number GSE42857 and GSE34426.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

5 Samples

Download data: BAM, BED

(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:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16809 GPL11154 GPL14954

16 Samples

Download data: TXT

(Submitter supplied) Genome-wide prefrontal cortex and cerebellum DNA methylation profiles of younger and older adult humans, captive chimpanzees, and captive rhesus macaques

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

44 Samples

Download data: IDAT

(Submitter supplied) Recent discussions of human brain evolution have largely focused on increased neuron numbers and changes in their connectivity and expression. However, it is increasingly appreciated that oligodendrocytes play important roles in cognitive function and disease. Whether both cell types follow distinctive evolutionary trajectories is not known. We examined the transcriptomes of neurons and oligodendrocytes in the frontal cortex of humans, chimpanzees, and rhesus macaques. more...

Organism:

Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21121 GPL18573 GPL21120

95 Samples

Download data: TXT