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Monodelphis domestica

ABSTRACT: Gray, short-tailed opossum (laboratory opossum)

PROVIDER: PRJNA12560 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR000090.fastq.gz	Fastqsanger.gz
	SRR000091.fastq.gz	Fastqsanger.gz
	SRR000092.fastq.gz	Fastqsanger.gz
	SRR000093.fastq.gz	Fastqsanger.gz

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Monodelphis domestica

Project description:Genome sequencing of gray short-tailed opossum (Monodelphis domestica)

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Monodelphis domestica isolate:mMonDom1

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Project description:Monodelphis domestica (gray short-tailed opossum) genome, mMonDom1, primary haplotype

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RNA-seq of 6 tissues from Monodelphis domestica to investigate the evolution of gene expression levels in mammalian organs

Project description:This experiment contains the subset of data corresponding to gray short-tailed opossum RNA-Seq data from experiment E-GEOD-30352 (http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352/), which goal is to understand the dynamics of mammalian transcriptome evolution. To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (∼3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (∼0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup.

2011-10-12 | E-MTAB-3719 | biostudies-arrayexpress

snRNA-seq of opossum (Monodelphis domestica) adult testis

Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 9,926 nuclei in opossum adult testis. This dataset includes three samples from three different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.

2021-11-08 | E-MTAB-11072 | biostudies-arrayexpress

Monodelphis domestica induced pluripotent stem cells reveal metatherian pluripotency architecture

Project description:Marsupials have been a powerful comparative model to understand mammalian biology. However, because of the unique characteristics of their embryology, marsupial pluripotency architecture remains to be fully understood, and nobody has succeeded in developing embryonic stem cells (ESCs) from any marsupial species. We have developed an integration-free induced pluripotent stem cell (iPSC) reprogramming method and established validated iPSC lines from two fully inbred strains of the gray short-tailed opossum (Monodelphis domestica). A comprehensive characterization of the M. domestica skin fibroblasts and their reprogrammed iPSCs was performed by genome-wide mRNA sequencing. The established monoiPSCs showed a significant (6,181 DE genes) but highly uniform (between clone r2 at 95% CI = 0.973 ± 0.007) resetting of the cellular transcriptome during reprogramming and were highly similar to eutherian ESCs and iPSCs in their overall transcriptomic and functional profiles. However, monoiPSCs showed unique regulatory architecture of the core pluripotency transcription factors and were more like epiblasts. Our results suggest POU5F1 and the splice variant specific expression of POU5F3 synergistically regulate the opossum pluripotency gene network. It is plausible that POU5F1, POU5F3 splice variant XM_016427856.1, and SOX2 form a self-regulatory network. NANOG expression, however, was specific to monoiPSCs and epiblasts, and displayed a distinct expression profile in embryonic cells. Furthermore, POU5F1 was highly expressed in trophectoderm cells, whereas all other pluripotency transcription factors were significantly downregulated, suggesting that the regulatory architecture of core pluripotency genes of marsupials may be distinct from that of eutherians.

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Project description:Age-dependent gene and protein expression following transection of neonatal spinal cord of Monodelphis domestica (South American Grey Short-tailed opossum)

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