GEO DataSets

(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) 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) 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; Homo sapiens; Macaca mulatta; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

4 related Platforms

422 Samples

Download data: CSV

(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:

Macaca mulatta; Pan troglodytes; Homo sapiens; Pan paniscus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26248

17 Samples

Download data: FA, GTF, MTX, RDS, TSV, 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:

Pan troglodytes; Macaca mulatta; Macaca nemestrina; Papio anubis; Homo sapiens; 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) 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:

Homo sapiens; Pan troglodytes; 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) 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:

GPL19148 GPL24149 GPL24148

3 Samples

Download data: HIC, TXT

(Submitter supplied) Understanding the evolutionary mechanisms underlying expansion and reorganization of the human brain is essential to comprehend the emergence of the cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closely related species (Homo sapiens; human, Pan troglodytes; chimpanzees and Pan paniscus; bonobos) can shed light onto neuronal changes occurring during evolution, the timing of their appearance and the role of evolutionary mechanisms favoring a particular type of cortical organization in humans. more...

Organism:

Pan paniscus; Homo sapiens; Pan troglodytes

Type:

Expression profiling by high throughput sequencing

6 related Platforms

15 Samples

Download data: TXT

(Submitter supplied) The placenta is arguably the most anatomically variable organ in mammals. Understanding gene expression patterns among placentas from multiple species can illuminate the molecular basis of placenta function as well as potentially enrich our knowledge of the biology of obstetrical syndromes. We measured the expression profiles of the term placenta of multiple therian mammals using RNA-Seq. We identified multiple genes and transcripts which are differentially expressed across lineages including prolactin, relaxin, and galectins, as well as identifying the non-housekeeping genes which are core to placenta function (such as components of annexin complexes) in all species studied.

Organism:

Loxodonta africana; Bos taurus; Dasypus novemcinctus; Ateles fusciceps; Mus musculus; Pan paniscus; Canis lupus familiaris; Monodelphis domestica

Type:

Expression profiling by high throughput sequencing

8 related Platforms

8 Samples

Download data: FASTA, FPKM_TRACKING

(Submitter supplied) Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human biology in health and disease. Similarly, iPSCs from closely related species should be a central tool to understand human evolution and to identify conserved and variable patterns of iPSC disease models. Here, we have generated human, gorilla, bonobo and cynomolgus monkey iPSCs. We show that these cells are well comparable in their differentiation potential and generally similar to human, cynomolgus and rhesus monkey embryonic stem cells (ESCs). more...

Organism:

Macaca mulatta; Gorilla gorilla; Homo sapiens; Pan paniscus; Macaca fascicularis

Type:

Expression profiling by high throughput sequencing

5 related Platforms

23 Samples

Download data: TSV

(Submitter supplied) Understanding cellular and molecular differences between human and non-human primates (NHPs) is essential to the basic comprehension of the evolution and diversity of our own species. Until now, preserved tissues have been the main source of most comparative studies between humans, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). However, these tissue samples do not fairly represent the distinctive traits of live cell behavior, are not amenable to genetic manipulation and do not allow translation of observed differences into phenotypical divergence. more...

Organism:

Pan troglodytes; Pan paniscus; Homo sapiens

Type:

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

Platforms:

GPL11154 GPL16809 GPL17238

18 Samples

Download data: TXT

(Submitter supplied) DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex diseases. These changes can be inherited through generations and likely have played an important role during human evolution. We performed a comparative analysis of CpG methylation patterns between humans and all great apes (chimpanzee, bonobo, gorilla and orangutan) on a total of 32 individuals.Our analysis identified ~1,000 genes with significantly altered methylation patterns among the great apes, including ~200 with a methylation pattern unique to humans. more...

Organism:

Gorilla gorilla gorilla; Pongo abelii; Gorilla beringei graueri; Pan paniscus; Pan troglodytes schweinfurthii; Pan troglodytes troglodytes; Pongo pygmaeus; Homo sapiens; Pan troglodytes verus

Type:

Methylation profiling by array

Platform:

GPL13534

32 Samples

Download data: TXT

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

Organism:

Arabidopsis thaliana; Sorghum bicolor; Caenorhabditis briggsae; Caenorhabditis elegans; Anopheles gambiae; Drosophila melanogaster; Drosophila pseudoobscura; Apis mellifera; Xenopus laevis; Xenopus tropicalis; Ateles geoffroyi; Gorilla gorilla; Bos taurus; Mus musculus; Rattus norvegicus; Human gammaherpesvirus 8; Macacine gammaherpesvirus 4; Saguinus labiatus; Tetraodon nigroviridis; Physcomitrium patens; Zea mays; Danio rerio; Macaca mulatta; Pan troglodytes; Pongo pygmaeus; human gammaherpesvirus 4; Gallid alphaherpesvirus 2; Schmidtea mediterranea; Betapolyomavirus macacae; Populus trichocarpa; Glycine max; Medicago truncatula; Gallus gallus; Pan paniscus; Ovis aries; Murid gammaherpesvirus 4; Oryza sativa; Saccharum officinarum; Bombyx mori; Lemur catta; Lagothrix lagotricha; Macaca nemestrina; Homo sapiens; Canis lupus familiaris; Sus scrofa; Human betaherpesvirus 5; Monodelphis domestica; Takifugu rubripes

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL10558 GPL6844

16 Samples

Download data: GPR

(Submitter supplied) Background: Similar to replicating myoblasts, many rhabdomyosarcoma cells express the myogenic determination gene MyoD. In contrast to myoblasts, rhabdomyosarcoma cells do not make the transition from a regulative growth phase to terminal differentiation. Previously we demonstrated that the forced expression of MyoD with its E-protein dimerization partner was sufficient to induce differentiation and suppress multiple growth-promoting genes, suggesting that the dimer was targeting a switch that regulated the transition from growth to differentiation. more...

Organism:

Physcomitrium patens; Populus trichocarpa; Glycine max; Bombyx mori; Lemur catta; Lagothrix lagotricha; Pan troglodytes; Sus scrofa; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus macacae; Arabidopsis thaliana; Oryza sativa; Saccharum officinarum; Caenorhabditis elegans; Anopheles gambiae; Apis mellifera; Danio rerio; Macaca mulatta; Gorilla gorilla; Pongo pygmaeus; Homo sapiens; Bos taurus; Gallid alphaherpesvirus 2; Macacine gammaherpesvirus 4; Tetraodon nigroviridis; Drosophila melanogaster; Drosophila pseudoobscura; Macaca nemestrina; Pan paniscus; Canis lupus familiaris; Ovis aries; Rattus norvegicus; Monodelphis domestica; Takifugu rubripes; Murid gammaherpesvirus 4; Medicago truncatula; Sorghum bicolor; Zea mays; Caenorhabditis briggsae; Xenopus laevis; Xenopus tropicalis; Gallus gallus; Ateles geoffroyi; Mus musculus; Human gammaherpesvirus 8; Saguinus labiatus; Schmidtea mediterranea

Type:

Non-coding RNA profiling by array

Platform:

GPL6844

4 Samples

Download data: GPR

(Submitter supplied) In animals, the maternal-to-embryonic transition (MET) is an important step occurring in the first days of early development. This important transition involves the degradation of maternal transcripts that have been stocked during oogenesis and used until this transition. Moreover, some precise and specific control mechanisms must govern the adequate synchronization of the MET events to promote embryonic genome activation. more...

Organism:

Saguinus imperator; Pan troglodytes; Bos taurus; Ovis aries; Rattus norvegicus; Lemur catta; Lagothrix; Macaca nemestrina; Canis lupus familiaris; Rhinopithecus bieti; Symphalangus syndactylus; Gorilla gorilla; Pongo abelii; Homo sapiens; Sus scrofa; Cricetulus griseus; Mus musculus; Ateles sp.; Macaca mulatta; Pan paniscus; Monodelphis domestica

Type:

Expression profiling by array

Platform:

GPL15194

1 Sample

Download data: TXT

(Submitter supplied) MicroRNAs are small non-coding RNAs that regulate a variety of biological processes. In the last version of the miRBase database (Release 17), 720 mouse microRNAs are accompanied by only 408 rat microRNAs. Given the importance of rat as a model organism, we used next generation sequencing and microarray technologies to discover novel microRNAs in rat kidneys.

Organism:

Danio rerio; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Equus caballus; Xenopus laevis; Macaca nemestrina; Canis lupus familiaris; Rattus norvegicus; Takifugu rubripes; Rhinopithecus bieti; Saguinus labiatus; Petromyzon marinus; Xenopus tropicalis; Ateles geoffroyi; Symphalangus syndactylus; Homo sapiens; Sus scrofa; Bos taurus; Mus musculus; Tetraodon nigroviridis; Oryzias latipes; Pan troglodytes; Pongo pygmaeus; Ovis aries; Taeniopygia guttata

Type:

Non-coding RNA profiling by array

Platform:

GPL14819

6 Samples

Download data: TXT

(Submitter supplied) Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. more...

Organism:

Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Monodelphis domestica; Gorilla gorilla; Homo sapiens; Mus musculus; Pan troglodytes; Pongo pygmaeus

Type:

Expression profiling by high throughput sequencing

10 related Platforms

131 Samples

Download data

(Submitter supplied) Intra-specific polymorphism in copy number is documented in many organisms, including human and chimpanzee, but very little is known for other great apes. This study aims to provide CNVs data for orangutan, gorilla, bonobo and chimpanzee, and compare the CNV patterns among these species, as well as with human CNVs and segmental duplications from public databases.

Organism:

Pongo abelii; Pan troglodytes troglodytes; Gorilla gorilla; Pongo pygmaeus; Pongo sp.; Homo sapiens; Gorilla gorilla gorilla; Pan paniscus; Pan troglodytes

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7749

58 Samples

Download data: PAIR, TXT

(Submitter supplied) MicroRNAs (miRNAs) are small noncoding RNAs that negatively regulate gene expression post-transcriptionally. They play a critical role in developmental and physiological processes and have been implicated in the pathogenesis of several diseases including cancer. To identify miRNA signatures associated with different stages of neoplastic development, we examined the expression profile of 776 primate miRNAs in the following cells: primary African green monkey kidney (pAGMK) cells; spontaneously immortalized, non-tumorigenic, low-passage VERO cells (10-87 LP); tumorigenic, high-passage VERO cells (10-87 HP); and a cell line (10-87 T) derived from a 10-87 HP cell tumor xenograft in athymic nude mice. more...

Organism:

Lemur catta; Lagothrix lagotricha; Macaca nemestrina; Homo sapiens; Chlorocebus aethiops; Macaca mulatta; Pan troglodytes; Pongo pygmaeus; Pan paniscus; Ateles geoffroyi; Gorilla gorilla; Saguinus labiatus

Type:

Non-coding RNA profiling by array

Platform:

GPL10649

9 Samples

Download data: TXT

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

Organism:

Gorilla gorilla; Pongo abelii; Pan troglodytes; Macaca mulatta; Pan paniscus; Pongo pygmaeus pygmaeus; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7749 GPL7748

47 Samples

Download data: PAIR