GEO DataSets

(Submitter supplied) Alternative splicing (AS) influences the expression of human genes in diverse ways. We previously used subcellular fraction-sequencing (Frac-Seq) to reveal an unexpected connection between alternative splicing and isoform-specific mRNA translation. Here we apply comparative transcriptomics to explore alternative splicing coupled translational control (AS-TC) across 13 million years of primate evolution. more...

Organism:

Pongo abelii; Homo sapiens; Pan troglodytes

Type:

Other

Platforms:

GPL23423 GPL20301 GPL24195

30 Samples

Download data: GTF, TSV

(Submitter supplied) Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee auto-tetraploids and allo-tetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23423 GPL27803 GPL20301

69 Samples

Download data: GTF, TXT

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

Organism:

Pan troglodytes; Callithrix jacchus; Pan paniscus; Homo sapiens

Type:

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

5 related Platforms

115 Samples

Download data: BW, HIC, RPKM, TXT

(Submitter supplied) Among primates, humans display a unique trajectory of development responsible for the many traits specific to our species. However, the inaccessibility of human and chimpanzee primary tissues has limited our ability to study human evolution. Comparative in vitro approaches using primate-derived induced pluripotent stem cells have begun to reveal species differences on the cellular and molecular levels. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

7 related Platforms

888 Samples

Download data: TXT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) hold promise for generating personalized xenogenic organs via development of cross-species chimeric animals. However, whether human and other primate iPSCs are capable of establishing cross-species chimeras remains unknown. Recognizing the ethical concerns of cross-species chimerism using human iPSCs, we explored the capacity for cross-species chimerism between distinct, non-human primates. more...

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes; Macaca nemestrina; Mus musculus

Type:

Expression profiling by high throughput sequencing

5 related Platforms

24 Samples

Download data: TSV

(Submitter supplied) Inter-individual variation in gene regulation has been shown to be heritable and it is quite often associated with differences in disease susceptibility between individuals. While many human studies focused on mapping associations between genetic and gene regulatory variation, much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. more...

Organism:

Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23423

38 Samples

Download data: TSV

(Submitter supplied) The human brain is about three times larger than the brain of our closest relatives, chimpanzees and bonobos. However, increased size alone fails to explain cognitive abilities unique to humans. Functional changes acquired in the human lineage are likely mediated by divergent gene expression and cell composition in brain regions. Here we generated a map of the human brain transcriptome by assessing the gene expression levels in 33 distinct regions representing all major brain structures from four adult cognitively healthy human individuals, three chimpanzees, three bonobos, and three rhesus macaques. more...

Organism:

Pan paniscus; Macaca mulatta; Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

422 Samples

Download data: CSV

(Submitter supplied) The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells. How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated. Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development. more...

Organism:

Pan troglodytes; Homo sapiens; Callithrix jacchus; Pan paniscus

Type:

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

5 related Platforms

115 Samples

Download data: BW, HIC, RPKM, TXT

(Submitter supplied) A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in speciation and adaptation. However, a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive. In primates, one of the crucial missing pieces of information towards a better understanding of regulatory evolution is a comparative annotation of interactions between distal regulatory elements and promoters. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Other

Platforms:

GPL20301 GPL23423

8 Samples

Download data: TXT

(Submitter supplied) Despite anatomical similarities, there are differences in susceptibility to cardiovascular disease (CVD) between primates; humans are prone to myocardial ischemia, while chimpanzees are prone to myocardial fibrosis. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) allow for direct inter-species comparisons of the gene regulatory response to CVD-relevant perturbations such as oxygen deprivation, a consequence of ischemia. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23423 GPL20301

84 Samples

Download data: TXT

(Submitter supplied) To better understand the evolution of primate adipose, we performed compartive analyses of adipose tissue from human, chimpanzee and macque adipose.

Organism:

Macaca mulatta; Homo sapiens; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23949 GPL20301 GPL23423

13 Samples

Download data: XLSX

(Submitter supplied) To study regulatory differences between species, the field of comparative primate genomics has used several approaches, including the use of post mortem frozen tissues, cell lines, and model organisms. However, there are limited quality cell lines from primates and post-mortem tissues cannot be staged, are not amenable to experimental perturbations and are often subject to high environmental variances. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL23423

211 Samples

Download data: CSV

(Submitter supplied) We compared a 5 week time course of cortical organoid differentiation across human, chimpanzee, orangutan, and rhesus using bulk RNAseq. In addition, single cell RNAseq was performed on a subset of time points from human cells in weeks 0, 1, 2, and 5.

Organism:

Pan troglodytes; Pongo abelii; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

55 Samples

Download data: GTF, TAR, TSV, TXT

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

Organism:

Homo sapiens; Pan troglodytes

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

107 Samples

Download data: TSV

(Submitter supplied) Human accelerated regions (HARs) are evolutionarily conserved sequences that acquired human-specific nucleotide changes and reside in genomic regions associated with unique human traits and disease. The majority of HARs (96%) are noncoding, a few of which have been shown to be functional enhancers. Here, we comprehensively tested human and chimpanzee sequences of HARs (N=714) for enhancer activity using a lentivirus-based massively parallel reporter assay (lentiMPRA) in human and chimpanzee iPSC derived neural progenitors at two differentiation time points. more...

Organism:

Pan troglodytes

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21121 GPL23423

50 Samples

Download data: NARROWPEAK, TSV

(Submitter supplied) There is substantial interest in the genetic regulatory framework that is established in early human development, and in the evolutionary forces that shaped early developmental processes in humans. Progress in these areas has been slow because it is difficult to obtain relevant biological samples. Recent technological developments in the generation and differentiation of inducible pluripotent stem cells (iPSCs) provide the ability to develop in vitro models of early human and non-human primates developmental stages. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23423 GPL20301

64 Samples

Download data: TXT