Gene expression profiles of induced pluripotent stem cells (iPSCs) and skin fibroblasts from orangutans
Ontology highlight
ABSTRACT:
ORGANISM(S): Pongo abelii Homo sapiens
PROVIDER: GSE69603 | GEO | 2015/06/10
SECONDARY ACCESSION(S): PRJNA285960
REPOSITORIES: GEO
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description: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. The overall goal was to evaluate gene expression biomarkers of pluripotency in iPSCs and skin fibroblasts derived from PBD-ZSD patients and healthy controls. Dermal fibroblast cultures from 2 orangutans were reprogrammed into iPSCs by transfection with retroviruses designed to express the human OCT4, SOX2, KLF4 and c-MYC cDNA. Fibroblasts and iPSCs were cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KOSR (knock-out serum replacement) at 37°C with 5% CO2 until confluence for RNA extraction. The overall goal was to evaluate gene expression biomarkers of pluripotency in iPSCs and original fibroblast cultures.
2015-06-10 | E-GEOD-69603 | biostudies-arrayexpress
Project description: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. In light of RNA sequencing analysis, generated gz-iPSCs robustly express genes associated with pluripotency and reprogramming processes, including epithelial-to-mesenchymal and mesenchymal-to-epithelial transitions (EMT-MET). Comparative transcriptomics with other species reveals patterns of gene expressions among mammalian PSCs and detects evolutionary conservation of pluripotency-associated genes and plausible importance of translation process. This work will aid in providing biological resource for this endangered species and enables new insight into the evolution of the mammalian PSCs.
2022-05-03 | GSE180619 | GEO
Project description:The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognized major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers.
2016-02-04 | GSE77508 | GEO
Project description:The northern white rhinoceros (NWR) is probably the earth’s most endangered mammal. To rescue the functionally extinct species, we aim to employ induced pluripotent stem cells (iPSCs) to generate gametes and subsequently embryos in vitro. To elucidate the regulation of pluripotency and differentiation of NWR PSCs, we generated iPSCs from a deceased NWR female using episomal reprogramming, and observed surprising similarities to human PSCs. NWR iPSCs exhibit a broad differentiation potency into the three germ layers and trophoblast, and acquire a naïve-like state of pluripotency, which is pivotal to differentiate PSCs into primordial germ cells (PGCs). Naïve culturing conditions induced a similar expression profile of pluripotency related genes in NWR iPSCs and human ESCs. Furthermore, naïve-like NWR iPSCs displayed increased expression of naïve and PGC marker genes, and a higher integration propensity into developing mouse embryos. As the conversion process was aided by ectopic BCL2 expression, and we observed integration of reprogramming factors, the NWR iPSCs presented here are unsuitable for gamete production. However, the gained insights into the developmental potential of both primed and naïve-like NWR iPSCs are fundamental for in future PGC-specification in order to rescue the species from extinction using cryopreserved somatic cells.
2021-12-01 | GSE161173 | GEO
Project description:The black-footed ferret (Mustela nigripes) is a star example of the efforts of conservation programs in bringing endangered species back from the brink of extinction. As one of the world’s most endangered mammals, the vast majority of black-footed ferrets living in the wild today are the offspring of a founding captive population. The success of this ongoing breeding program, however, is threatened by inbreeding depression and the observed decline in pregnancy rates since its founding. As the wild and modern captive populations share a genetic history, the greatest difference between the two groups is the captive environment of the breeding program. In this study, we used RNA sequencing and proteomics for the first time in black-footed ferrets to explore whether the diet of wild ferrets versus captive diet variants could explain the differences in fertility and sperm characteristics observed between each population. We find that changes in both the transcriptional and proteomic profile of black-footed ferret ejaculate are strongly associated with differences in fertility, especially in pathways associated with innate immunity and metabolism; that transcriptional changes are further exacerbated by diet. Overall, our results support the hypothesis of ongoing environmental-dependent inbreeding depression in the black-footed ferret, with a need to re-evaluate dietary and environmental parameters of the conservation program; and also illustrates the value of multi-level genomics for conservation management programs.
2023-09-20 | PXD044152 | Pride
Project description:Spotted seals (Phoca largha) is a critically endangered pinniped in China and South Korea. Captive in artificially controlled environment is a conventional method to protect and maintain the population of this species. However, little is known about the physiological differences between the wild and captive P. largha. In order to draw the preliminary protein expression profile in the P. largha, blood from the wild and captive pups were subjected to a label-free comparative proteomic analysis. According to the results, 972 proteins were identified, which performed functions related to various metabolic, immune and cellular processes. Among these identified proteins, the expression level of 51 proteins significantly changed between the wild and captive P. large pups. These differentially expressed proteins were enriched in a wide range of cellular functions, including cytoskeleton, phagocytosis. proteolysis, gene expression regulation and carbohydrate metabolism. The activities of phagocytosis and its related ubiquitin mediated proteolysis were significantly higher in the blood of wild P. largha pups than in captive individuals. In addition, a key protein associated with the differences in the wild and captive P. largha pups, heat shock protein 90-beta, were determined due to the most interactions of it with various differentially expressed proteins. Moreover, the wild P. largha pups could be more nutritionally stressed and have more powerful immune capacity. Our study provides the first data on the preliminary protein composition and gives useful information for the physiological characteristics research in this species.
2021-09-09 | PXD020112 | Pride
Project description:In this study two Viperidae species, living in two different habitats, the horned desert viper (Cerastes cerastes) native to the deserts in North Africa and in turn the mangrove pit viper (Cryptelytrops purpureomaculatus), which can be found in South/Southeast Asia, were studied in terms of the identification of the venom proteome.
2018-08-07 | MSV000082753 | MassIVE
Project description:Southeast Asian pandemic strain
| PRJNA33623 | ENA
Project description:The giant panda (Ailuropoda melanoleuca) stands as a flagship and umbrella species, symbolizing global biodiversity. While traditional assisted reproductive technology faces constraints in safeguarding the genetic diversity of giant pandas and bolstering the population size of giant pandas, induced pluripotent stem cells (iPSCs) known for their capacity to differentiate into diverse cells types, including germ cells, present a transformative potential for conservation of endangered animals. In our study, we isolated primary fibroblast cells from an individual giant panda and successfully generated giant panda induced pluripotent stem cells (GPiPSCs) through a non-integrating episomal vectors reprogramming method. Characterization of these GPiPSCs revealed their state of primed pluripotency and demonstrated their potential for differentiation. Furthermore, we innovatively formulated a species-specific chemically defined FACL medium and unraveled the intricate signaling pathway networks responsible for maintaining the pluripotency and fostering cell proliferation of GPiPSCs. This study provides key insights into rare species iPSCs, offering materials for panda characteristics research and laying the groundwork for in vitro giant panda gamete generation, potentially aiding endangered species conservation.
2024-09-25 | GSE250292 | GEO