GEO DataSets

(Submitter supplied) The foundation of many human-specific traits is likely established during early embryonic development. To understand these molecular processes, we compared gene expression dynamics in embryoid bodies (EBs) differentiated from iPSCs of four primate species: human, orangutan, cynomolgus, and rhesus macaque. We performed scRNA-seq on ∼ 85,000 cells after 8 and 16 days of EB differentiation, identifying diverse cell types across all three germ layers. more...

Organism:

Pongo abelii; Macaca fascicularis; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL35048 GPL35050 GPL35049

10 Samples

Download data: H5

(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) Comparing the molecular and cellular properties among primates is crucial to better understand human evolution and biology. However, it is difficult or ethically even impossible to collect matched tissues from many primates, especially during development. An alternative is to model different cell types and their development using induced pluripotent stem cells (iPSCs). These can be generated from many tissue sources, but non-invasive sampling would decisively broaden the spectrum of non-human primates that can be investigated. more...

Organism:

Homo sapiens; Pongo abelii; Gorilla gorilla

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28987 GPL18460 GPL28986

42 Samples

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

Type:

Expression profiling by high throughput sequencing

14 related Platforms

197 Samples

Download data: TXT

(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:

Pongo abelii; Pan troglodytes; Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

5 related Platforms

55 Samples

Download data: GTF, TAR, TSV, TXT

(Submitter supplied) In the present study we analyzed centromeric localization on chromosome 12 in different orangutan and results showed that each individual exhibits a different arrangement of CENP-A binding domains.

Organism:

Pongo pygmaeus; Homo sapiens; Pongo abelii

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL21737 GPL21736

4 Samples

Download data: GFF, PAIR

(Submitter supplied) Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases - about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via non-allelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. more...

Organism:

Papio anubis; Pan troglodytes; Macaca mulatta; Gorilla gorilla; Pongo abelii; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL21019

32 Samples

Download data: TXT

(Submitter supplied) Orangutans are an endangered species whose natural habitats are restricted to the Southeast Asian islands of Borneo and Sumatra. For potential species conservation and functional genomics studies, we derived induced pluripotent stem cells (iPSCs) from cryopreserved skin fibroblasts obtained from captive orangutans. We report the gene expression profiles of iPSCs and skin fibroblasts derived from orangtuans.

Organism:

Homo sapiens; Pongo abelii

Type:

Expression profiling by array

Platform:

GPL571

8 Samples

Download data: CEL

(Submitter supplied) While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. more...

Organism:

Macaca mulatta; Pan troglodytes; Pongo pygmaeus; Pongo abelii

Type:

Genome variation profiling by genome tiling array

30 related Platforms

30 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:

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

Type:

Methylation profiling by array

Platform:

GPL13534

32 Samples

Download data: TXT

(Submitter supplied) Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.

Organism:

Macaca mulatta; Homo sapiens; Pongo abelii; Gorilla beringei; Pan troglodytes

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14930

17 Samples

Download data: TXT

(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:

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

Type:

Expression profiling by array

Platform:

GPL15194

1 Sample

Download data: TXT

(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:

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

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7749

58 Samples

Download data: PAIR, TXT

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

Organism:

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

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7749 GPL7748

47 Samples

Download data: PAIR

(Submitter supplied) Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. more...

Organism:

Pan troglodytes; Pongo pygmaeus pygmaeus; Homo sapiens; Pongo abelii

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7748 GPL7749

24 Samples

Download data: PAIR

(Submitter supplied) Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. more...

Organism:

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

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7749 GPL7748

23 Samples

Download data: PAIR