Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Establishment of Giant Panda Induced Pluripotent Stem Cells

ABSTRACT: 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.

ORGANISM(S): Ailuropoda melanoleuca

PROVIDER: GSE250292 | GEO | 2024/09/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Giant panda (Ailuropoda melanoleuca) gut microbiomes degrade bamboo in distinct patterns: heterofermentation of green leaves to ethanol, lactate and acetate, and homofermentation of yellow pith to lactate

Project description:The iconic giant panda is an endangered species known worldwide for its peculiar dietary habits. While retaining the digestive system of a carnivore, the giant panda successfully moved into a diet almost exclusively based on bamboo. Digestion of lignocellulose is believed to be conducted solely by its gut microbiome, provided that no lignocellulose-degrading enzyme was found in the giant panda’s genome. Many reports focused on which lignocellulose component feeds the giant panda, while little effort was made to link the products of bamboo fermentation to the panda’s dietary choices. In the present study, fermentation of either green leaves or yellow pith was conducted in the laboratory using gut microbiomes derived from either green or yellow stools, respectively. Green leaves were fermented to ethanol, lactate and acetate, while yellow pith to lactate resembling, respectively, hetero/homo-fermentation patterns. Several microbial pathways (assessed by metaproteomics) related to hemicellulose rather than cellulose degradation. However, alpha-amylases (E.C. 3.2.1.1) from the giant panda itself were the most predominant enzyme (up to 60% of all metaproteins), indicating that they have a primary role in bamboo digestion. The distinct fermentation profiles resulting from digestion of selected portions of bamboo may be part of the feeding strategy of giant pandas.

2020-03-02 | PXD010872 | Pride

Transcriptome profiling across five tissues of giant panda

Project description:Gene differential expression studies can serve to explore and understand the laws and 16 characteristics of animal life activities, and the difference in gene expression between different 17 animal tissues have been well demonstrated and studied. However, for the world-famous rare 18 and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood 19 and spleen has been reported separately. Here, in order to explore the transcriptome differences 20 between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, 21 lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 22 platform. The comparative analysis of the inter-tissue gene expression patterns was carried out 23 based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, 24 Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction 25 (PPI) network were performed according to the identified differentially expressed genes (DEGs). 26 We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 27 18,701 genes, including 3492 novel genes. With corrected p-value < 0.05 and |log2FoldChange| > 28 2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, 29 lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and 30 ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the 31 spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI 32 network. The results of the analyses showed a similar gene expression pattern between the spleen 33 and lung. This study provided for the first time the heart, liver, lung, and kidney’s transcriptome 34 resources of the giant panda, and it provided a valuable resource for further genetic research or 35 other potential research.

2020-08-31 | GSE138294 | GEO

Generation and gene expression profiles of Grevy’s zebra iPSCs

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

Exosomal microRNAs in the giant panda (Ailuropoda melanoleuca) breast milk: the potential maternal regulators for the development of newborn cubs

Project description:Purpose:To present the miRNA expression profiles in giant panda milk exosomes across five lactation stages (0, 3, 7, 15 and 30 days after birth), aiming to provide new information for investigations into the physiological functions of the giant panda milk Methods: Three females were sampled in all, and each individual were sampled over multiple lactations, including 0, 3, 7, 15 and 30 days after delivery. Breast milk samples (5-10 ml) were collected from each stages. Total RNA isolated from individuals in five lactation stages (0, 7, 15 and 30 days after delivery) were pooled in equal quantities for each stage Results: Here, we illustrated the species and expression characteristics of exosome-loaded miRNAs existing in giant panda breast milk during distinct lactation periods, and highlighted the enrichment of immune- and development-related endogenous miRNAs in colostral and mature giant panda milk, which are stable even in certain hash conditions, like low pH and high concentration of RNAase, by the protection of extracellular vesicles.These findings indicate that breast milk may allow dietary intake of maternal miRNAs by infants for the regulation of postnatal development. We also demonstrated that the exogenous plant miRNA from the primary food source of giant panda (bamboo) were detected in the exosomes of giant panda breast milk, which were predicted to be of regulatory role in basic cell metabolism and neuron development. This result suggested that the dietary plant miRNAs were able to be absorbed by host cell and then secreted to body fluids as potential cross-kingdom regulators. Conclusions: Exosomal miRNAs in the giant panda breast milk may be the crucial maternal regulators for the development of intrinsic ‘slink’ newborn cubs.

2017-06-01 | GSE89755 | GEO

Comparative analysis of piRNA profiles reveals cryoinjury or freezability between boar (Sus scrofa) and giant panda (Ailuropoda melanoleuca) sperm during cryopreservation

Project description:In this study, differentially expressed (DE)piRNAs of fresh and frozen-thawed sperm with different freeze tolerance compacity from giant panda and boar were evaluated. The results showed 1160 (22 down-regulated and 1138 up-regulated) and 384 (110 up-regulated and 274 down-regulated) differentially expressed (DE) piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE mRNAs of DE piRNAs were mainly enriched in biological regulation, cellular process and metabolic process in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed on DNA replication and cAMP signaling pathway in giant panda, but cAMP, cGMP and MAPK signaling pathway in boar sperm which were considered as part of olfactory transduction pathway.Conclusion:Olfactory transduction related pathways maybe contributed to different freeze tolerance compacity between giant panda and boar sperm, which will benefit to further understand the molecular mechanism of sperm cryoinjury and freezability.

2021-04-19 | GSE163128 | GEO

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences

Project description:Ursids (bears) in general, and giant pandas in particular, are highly altricial at birth. The components of bear milks and their changes with time may be uniquely adapted to nourish relatively immature neonates, protect them from pathogens, and support the maturation of neonatal digestive physiology. Serial milk samples collected from three giant pandas in early lactation were subjected to untargeted metabolite profiling and multivariate analysis. Changes in milk metabolites with time after birth were analysed by Principal Component Analysis, Hierarchical Cluster Analysis and further supported by Orthogonal Partial Least Square-Discriminant Analysis, revealing three phases of milk maturation: days 1–6 (Phase 1), days 7–20 (Phase 2), and beyond day 20 (Phase 3). While the compositions of Phase 1 milks were essentially indistinguishable among individuals, divergences emerged during the second week of lactation. OPLS regression analysis positioned against the growth rate of one cub tentatively inferred a correlation with changes in the abundance of a trisaccharide, isoglobotriose, previously observed to be a major oligosaccharide in ursid milks. Three artificial milk formulae used to feed giant panda cubs were also analysed, and were found to differ markedly in component content from natural panda milk. These findings have implications for the dependence of the ontogeny of all species of bears, and potentially other members of the Carnivora and beyond, on the complexity and sequential changes in maternal provision of micrometabolites in the immediate period after birth.

2015-03-31 | MTBLS165 | MetaboLights

Gene expression profiles of induced pluripotent stem cells (iPSCs) and skin fibroblasts from orangutans

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

giant panda gut

Project description:giant panda gut Raw sequence reads

| PRJNA547451 | ENA

Gene expression profiles of induced pluripotent stem cells (iPSCs) and skin fibroblasts from orangutans

2015-06-10 | GSE69603 | GEO

Proteome validation for novel full-length genes in the giant panda

Project description:we applied RNA-seq to detect novel expressed transcripts in 12 tissues of giant pandas, using a transcriptome reconstruction strategy combining reference-based and de novo methods. Then we used mass spectrometry method to identify proteomes of five selected tissues, aiming at validating these novel full-length genes we identified.

2015-12-23 | PXD002917 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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