GEO DataSets

(Submitter supplied) Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether changes in human cells alter requirements for essential genes. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19148 GPL16791

36 Samples

Download data: 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:

Homo sapiens; Macaca mulatta; Pan troglodytes

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:

Homo sapiens; Pan troglodytes; Macaca mulatta

Type:

Genome binding/occupancy profiling by high throughput sequencing

6 related Platforms

12 Samples

Download data: MTX, RDS, TXT, XLSX

(Submitter supplied) We carried out cell-type specific whole genome bisulfite sequencing from primate brains (orthologous region to human BA46) that underwent fluorescence-activated nuclei sorting (FANS).

Organism:

Macaca mulatta; Pan troglodytes

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19129 GPL19148

50 Samples

Download data: TXT

(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:

Macaca mulatta; Pan troglodytes

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) Brain development is exceptionally delayed in humans compared to nonhuman primates (NHPs), a finding often termed neoteny. Signatures of neoteny, including a protracted proliferation of apical and basal progenitors as well as a delay in physiological activity of mature neurons, have been revealed in part through the use of induced pluripotent stem cell (iPSC) modeling of primate neurogenesis. IPSC modeling is particularly useful when examining the molecular drivers of a cellular phenotype such as gene transcription. more...

Organism:

Macaca mulatta; Pan troglodytes; Homo sapiens; Gorilla; Pan paniscus

Type:

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

10 related Platforms

79 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) Here, we performed RNA-Seq on mRNA isolated from primary dermal fibroblasts of human, mice and multiple non-human primate species transfected with polyinosinic-polycytidylic acid (polyI:C), a synthetic dsRNA analog that invokes a strong interferon-mediated response, or mock transfected.

Organism:

Macaca mulatta; Macaca nemestrina; Papio anubis; Homo sapiens; Pan troglodytes; Saimiri sciureus; Gorilla gorilla; Pongo abelii; Mus musculus; Pan paniscus

Type:

Expression profiling by high throughput sequencing

14 related Platforms

197 Samples

Download data: TXT

(Submitter supplied) We developed a continuous-trait probabilistic model to identify genome-wide evolutionary patterns of 3D genome structures based on multi-species Hi-C data. We applied the proposed method to analyzing cross-species Hi-C data from the same cell type in multiple primate species. The results showed that the proposed method enables discovery of distinct Hi-C contact frequency evolutionary patterns across species.

Organism:

Pan paniscus; Gorilla gorilla; Pan troglodytes

Type:

Other

Platforms:

GPL24149 GPL19148 GPL24148

3 Samples

Download data: HIC, TXT

(Submitter supplied) Direct comparisons of human and non-human primate brain tissue have the potential to reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is largely inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL19148 GPL19129 GPL16791

3096 Samples

Download data: TXT, XLSX

(Submitter supplied) Changes in gene regulation have been shown to contribute to phenotypic differences between closely related species, most notably in primates. It is likely that a subset of inter-species regulatory differences can be explained by changes in chromatin accessibility and transcription factor binding, yet there is a paucity of comparative data sets with which to investigate this. Using ATAC-seq, we profiled genome-wide chromatin accessibility in a matched set of 6 human and 6 chimpanzee (Pan troglodytes, our closest living relative) induced pluripotent stem cells from which we have previously collected gene expression data. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19148 GPL16791

12 Samples

Download data: TXT

(Submitter supplied) A long-standing hypothesis is that changes in gene regulation play an important role in adaptive evolution, notably in primates. Yet, in spite of the evidence accumulated in the past decade that regulatory changes contribute to many species-specific adaptations, we still know remarkably little about the mechanisms of regulatory evolu tion. In this study we focused on DNA methylation, an epigenetic mechanism whose contribution to the evolution of gene expression remains unclear. more...

Organism:

Homo sapiens; Macaca mulatta; Pan troglodytes

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL19148 GPL19129 GPL16791

159 Samples

Download data: RDA, TXT

(Submitter supplied) We developed a probabilistic method to simultaneously infer genome-wide heterogeneous evolutionary states. We applied the proposed method to analyze a cross-species DNA replication timing (RT) dataset from the same cell type in five primate species. We demonstrated that the proposed model enables discovery of genomic regions with distinct evolutionary patterns of RT.

Organism:

Chlorocebus aethiops; Homo sapiens; Pan troglodytes; Pongo pygmaeus; Nomascus leucogenys

Type:

Other

5 related Platforms

5 Samples

Download data: BW

(Submitter supplied) We couple long-read sequence assembly, full-length cDNA sequencing, and a multi-platform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies where most genes are complete, gaps are closed, and novel gene models are identified. We further analyzed the overlap between structural variants in the human genome and gene expression differences in human and chimpanzee cells, including iPS-derived organoid radial glia cells.

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19148

117 Samples

Download data: TXT

(Submitter supplied) Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription.  To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee and rhesus macaque. more...

Organism:

Pan troglodytes; Homo sapiens; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19148 GPL19129 GPL16791

14 Samples

Download data: TXT

(Submitter supplied) Transposable elements (TEs) comprise a substantial proportion of primate genomes. Because of the potential deleterious effects of TEs during development, TEs are targeted for silencing by sequence-specific KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, acquire mutations to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19148 GPL16791

17 Samples

Download data: TXT

(Submitter supplied) Transposable elements (TEs) comprise a substantial proportion of primate genomes. Because of the potential deleterious effects of TEs during development, TEs are targeted for silencing by sequence-specific KRAB-ZNF proteins, which recruit the TRIM28-SETDB1 complex, to deposit the repressive histone modification H3K9me3. TEs, in turn, acquire mutations to evade detection by the host, and hence KRAB-ZNF proteins need to rapidly evolve to counteract them. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL19148

34 Samples

Download data: TXT

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

Organism:

Homo sapiens; Pan troglodytes

Type:

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

Platforms:

GPL19148 GPL16791

51 Samples

Download data