GEO DataSets

(Submitter supplied) Comparative studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19148

28 Samples

Download data: TXT

(Submitter supplied) Comparative genomics studies in primates are extremely restricted due to our limited access to samples from non-human apes. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. more...

Organism:

Homo sapiens; Pan troglodytes

Type:

Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platform:

GPL19148

9 Samples

Download data: BED, TXT

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

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing; Methylation profiling by array; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Platforms:

GPL16791 GPL13534 GPL19148

65 Samples

Download data: BED

(Submitter supplied) Comparative studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

28 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:

Macaca mulatta; Pan troglodytes; Homo sapiens

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) 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:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL23423

211 Samples

Download data: CSV

(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) 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

(Submitter supplied) Macrophages are important target cells for diverse viruses, and thus represent a valuable model system for studying virus biology. Isolation of primary human macrophages is done by culture of dissociated tissues or from differentiated blood monocytes, but these methods are both time consuming and result in low numbers of recovered macrophages. Here, we explore whether macrophages derived from human induced pluripotent stem cells (iPSCs)—which proliferate indefinitely and potentially provide unlimited starting material— could serve as a faithful model system for studying virus biology. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

28 Samples

Download data: CSV, GTF

(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:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL23423

84 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by genome tiling array

Platforms:

GPL10558 GPL13534

48 Samples

Download data: IDAT

(Submitter supplied) Analysis of contribution of cell type of origin and individual to gene expression differences in iPSCs. The hypothesis tested in the present study was that cell type of origin affects iPSC gene expression. Results show that individual has a much stronger effect than cell type of origin on differences between iPSCs derived from multiple individuals.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

24 Samples

Download data: IDAT

(Submitter supplied) Analysis of contribution of cell type of origin and individual to gene expression differences in iPSCs. The hypothesis tested in the present study was that cell type of origin affects iPSC gene expression. Results show that individual has a much stronger effect than cell type of origin on differences between iPSCs derived from multiple individuals.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: TXT

(Submitter supplied) Our recent approach to induction of pluripotent stem cells from fibroblasts using protein extract from mouse ESCs could overcome the potential tumorigenicity risks associated with random retroviral integration. Here we examine the epigenetic modifications and transcriptome in two kinds of iPSCs and a partially reprogrammed iPSC (iPSCp) generated from adult cardiac and skin fibroblasts independently to assess any perturbations of transcription program during reprogramming.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11002

14 Samples

Download data: BEDGRAPH

(Submitter supplied) Gene expression study of human and Chimpanzee iPS cell.

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by array

Dataset:

GDS5443

Platform:

GPL570

7 Samples

Download data: CEL

Analysis of chimpanzee iPSCs generated from blood cells using Sendai virus vector TS12KOS which carries reprogramming factors KLF4, OCT3/4, and SOX2. TS12KOS was also used to establish human iPSCs from fibroblasts. Results examine differentially expressed genes between human and chimpanzee iPSCs.

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by array, transformed count, 2 cell type, 5 individual, 2 species sets

Platform:

GPL570

Series:

GSE62572

7 Samples

Download data: CEL

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

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27803

22 Samples

Download data

(Submitter supplied) We evaluated the degree to which gene expression patterns in primate skeletal cells differ across cell types and species. First, we optimized differentiation protocols of human and chimpanzee iPSCs through an intermediate MSC state and into osteogenic cells. Single-cell RNA sequencing was collected from each stage of differentiation (iPSCs, MSCs, and osteogenic cells) using the 10X Genomics platform to characterize gene expression variation.

Organism:

Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27803

18 Samples

Download data: CSV

(Submitter supplied) We evaluated the degree to which gene expression patterns in primate skeletal cells differ across cell types and species. First, we optimized differentiation protocols of human and chimpanzee iPSCs through an intermediate MSC state and into chondrogenic or osteogenic cells. Single-cell RNA sequencing was collected from each stage of differentiation (iPSCs, MSCs, chondrogenic cells, and osteogenic cells) using the 10X Genomics platform to characterize gene expression variation.

Organism:

Pan troglodytes; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27803

4 Samples

Download data: CSV

(Submitter supplied) Induced pluripotent stem cells (iPSCs) can provide biological resource for functional and conservation research for various species. However, the understanding of species variations of mammalian iPSCs is still limited. Here, we report the first generation of iPSCs from the endangered species Grevy's zebra (Equus grevyi; gz-iPSCs). We reprogram primary fibroblasts with human reprogramming transcription factors, OCT3/4, SOX2, KLF4, and c-MYC, with the retroviral method and confirmed the pluripotency and differentiation potential. more...

Organism:

Equus grevyi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30418

6 Samples

Download data: TSV