Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reconstruction of an Orangutan reference genome

ABSTRACT: orangutan BACs Genome sequencing and assembly

PROVIDER: PRJNA646518 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

ChIP-chip from four orangutan cells with CENP-A

Project description: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.

2017-01-01 | GSE81003 | GEO

Bonobo, Gorilla, Sumatran orangutan

Project description:Bonobo (Pan paniscus), Sumatran orangutan (Pongo abelii) Y chromosome sequencing and assembly and the improvement of the gorilla Y draft assembly

| PRJNA602326 | ENA

High-resolution comparative analysis of great ape genomes

Project description: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.

2018-06-12 | GSE113931 | GEO

Cross-species multi-omic analyses of great ape ejaculates reveal novel strategies for enhancing sperm cryopreservation in Bornean orangutan (Pongo pygmaeus)

Project description:The orangutan (Pongo spp., Linnaeus, 1760) is the most endangered great ape, classified as critically endangered. Sperm cryopreservation is a valuable tool for banking genetic resources and solving the complexities of relocating animals; however, cryopreservation protocols remain suboptimal for this species. Due to their phylogenetic closeness, this study aimed to explore the applicability of a chimpanzee (Pan troglodytes, Blumenbach, 1775) sperm cryopreservation protocol to orangutans. To guide further modifications to the protocol, we revealed, for the first time, the comprehensive lipidomic and proteomic characterizations of orangutan ejaculates with parallel comparisons to chimpanzee ejaculates. Functional analyses of oxidative and osmotic stress responses were also conducted to provide valuable evidence of the physiological changes and defense mechanisms associated with sperm cryodamage. The cross-species multi-omic analyses showed that compared to chimpanzee, the orangutan sperm lipid profile presented significant alterations after the freezing-thawing process, notably showing significant cholesterol loss. While interspecies differences in antioxidant enzyme composition and activity were observed, insufficient evidence supported the orangutan's heightened susceptibility to oxidative stress. Conversely, orangutan sperm exhibited low tolerance to hypoosmotic conditions. To prevent cryodamage, a modified thawing protocol by implementing a serial dilution approach significantly minimized the hypoosmotic shock and improved post-thaw motility to 19%. In conclusion, this study presents the first complete proteome and lipidome analyses of chimpanzee and orangutan ejaculates, providing valuable insights into the physiological changes and defense mechanisms associated with sperm cryopreservation. This knowledge enabled a science-based approach to improving cryopreservation protocols, moving away from trial-and-error methods.

2026-03-08 | PXD073407 | Pride

ATAC-seq of gorilla (Gorilla gorilla), orangutan (Pongo abelii) and cynomolgus macaque (Macaca fascicularis) iPSC, KRAB-dCas9 iPSC and iPSC-derived NPC cell lines

Project description:To compare chromatin accessibility across three primate species, between wild-type (WT) and genetically modified induced pluripotent stem cell (iPSC) lines, and between the iPSC state and neural precursor cells (NPCs) derived from these iPSCs, we generated ATAC-seq data from nine primate samples. The samples included two gorilla WT iPSC samples and one gorilla KRAB-dCas9 iPSC sample (all from the same individual), one orangutan WT iPSC sample, one orangutan KRAB-dCas9 iPSC sample and two orangutan NPC samples (from two different individuals), and one cynomolgus macaque WT iPSC sample and one cynomolgus macaque KRAB-dCas9 iPSC sample (from the same individual). The gorilla and orangutan iPSCs were derived from urinary stem cells (Geuder et al. 2021), while the cynomolgus macaque iPSCs were derived from skin-fibroblasts. The KRAB-dCas9 iPS cell lines were created by stably integrating dox-inducible KRAB-dCas9-HA-P2A-mCherry construct at the AAVS1 locus (Edenhofer et al. 2024). NPCs were obtained by the directed differentiation of iPSCs via dual-SMAD inhibition (Chambers et al. 2009; Ohnuki et al. 2014). ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.

2025-10-30 | E-MTAB-15654 | biostudies-arrayexpress

Genome wide expression patterns of 19 human urinary cells as well as 6 primary urinary cells and 17 corresponding iPSCs of human, gorilla and orangutan

Project description: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. Here, we report the generation of primate iPSCs from urine samples. We first validate and optimize the procedure using human urine samples and show that Sendai virus transduction of reprogramming factors into urinary cells efficiently generates integration-free iPSCs, which maintain their pluripotency under feeder-free culture conditions. We demonstrate that this method is also applicable to gorilla and orangutan urinary cells isolated from a non-sterile zoo floor. We characterize the urinary cells, iPSCs and derived neural progenitor cells using karyotyping, immunohistochemistry, differentiation assays and RNA-sequencing. We show that the urine-derived human iPSCs are indistinguishable from well characterized PBMC-derived human iPSCs and that the gorilla and orangutan iPSCs are well comparable to the human iPSCs. In summary, this study introduces a novel and efficient approach to generate primate iPSCs non-invasively from urinary samples.

2020-08-31 | GSE155889 | GEO

Bonobo and Bornean orangutan

Project description:Testis RNA-Seq datasets from bonobo (Pan paniscus) and Bornean orangutan (Pongo pygmaeus pygmaeus) for the assembly and expression of Y-chromosomal ampliconic genes

| PRJNA587108 | ENA

Human embryonic stem cell, chimpanzee induced pluripotent stem cell, orangutan induced pluripotent stem cell, rhesus embryonic stem cell, and their derived cortical organoid RNA-seq

Project description: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.

2018-05-31 | GSE106245 | GEO

ChIP-chip from four orangutan cells with CENP-A

Project description:ChIP-chip from four orangutan cells with CENP-A

| PRJNA320260 | ENA

Long-read RNA-seq of human (Homo sapiens), gorilla (Gorilla gorilla), orangutan (Pongo abelii) and cynomolgus macaque (Macaca fascicularis) induced pluripotent stem cell and neural precursor cell lines

Project description:We generated Oxford Nanopore long-read RNA-seq data to compare transcript isoform usage across four primate species and two cell types. We profiled induced pluripotent stem cells (iPSCs) and iPSC-derived neural precursor cells (NPCs) from human (Homo sapiens), gorilla (Gorilla gorilla), orangutan (Pongo abelii), and cynomolgus macaque (Macaca fascicularis).

2026-03-31 | GSE326106 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data