Ontology highlight
ABSTRACT:
PROVIDER: PRJNA743944 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15046087_1.fastq.gz | Fastqsanger.gz | |||
| SRR15046087_2.fastq.gz | Fastqsanger.gz | |||
| SRR15046088_1.fastq.gz | Fastqsanger.gz | |||
| SRR15046088_2.fastq.gz | Fastqsanger.gz | |||
| SRR15046089_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:The OK cell line derived from kidney of a female opossum Didelphys virginiana has proven to be a useful model in which to investigate the unique regulation of ion transport and membrane trafficking mechanisms in the proximal tubule (PT). Sequence data and comparison of the transcriptome of this cell line to eutherian mammal PTs would further broaden the utility of this culture model. However, genomic sequence for Didelphys virginiana is not available and although a draft genome sequence for the opossum Monodelphis domestica (sequenced in 2012 by the Broad Institute) exists, its relatedness and similarity of the transcriptome to the Didelphys virginiana species is not known. The Monodelphis domestica sequence is not highly annotated, and the majority of transcripts are predicted rather than experimentally validated. Using deep RNA sequencing of the Didelphys virginiana OK cell line we characterized its transcriptome using de novo transcriptome assembly and alignment to the Monodelphis domestica genome. The quality of the de novo assembled transcriptome was assessed by the extent of homology to sequences in nucleotide and protein databases. Gene expression levels in the OK cell line, from both the de novo transcriptome and genes aligned to the Monodelphis domestica genome, were compared to publicly available rat kidney nephron segment expression data. Our studies demonstrate the expression in OK cells of numerous PT specific ion transporters and other key proteins relevant for rodent and human PT function. The sequence and expression data reported here provide a new and important resource for studies on the regulation of PT mRNA and protein expression.
2017-08-07 | GSE94443 | GEO
Project description:Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. The majority (152/176) of X-linked genes exhibited paternally imprinted expression with nearly 100% maternal allele expression, whereas 24 loci (14%) escaped inactivation showing varying levels of biallelic expression. In addition to regulation by the non-coding RSX transcript, strong depletion of H3K27me3 at escaper gene loci indicates that histone states also influence opossum XCI. Notably, the opossum does not show an association between X-linked gene expression and promoter DNA methylation. Our study provides the first comprehensive catalogue of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals. Profiling of four histone modifications in embryonic day 13 opossum (Monodelphis domestica) fetal brain by Illumina ChIP-seq
2013-09-23 | E-GEOD-45186 | biostudies-arrayexpress
Project description:Multiple mammalian lineages independently evolved a definitive mammalian middle ear (DMME) through breakdown of Meckel’s cartilage (MC). However, the cellular and molecular drivers of this evolutionary transition remain unknown for most mammal groups. Here, we identify such drivers in the living marsupial opossum Monodelphis domestica, whose MC transformation during development anatomically mirrors the evolutionary transformation observed in fossils. Specifically, we link increases in cellular apoptosis and TGF-BR2 signalling to MC breakdown in opossums. We demonstrate that a simple change in TGF-b signalling is sufficient to inhibit MC breakdown during opossum development, indicating that changes in TGF-b signalling might be key during mammalian evolution. Furthermore, the apoptosis that we observe during opossum MC breakdown does not seemingly occur in mouse, consistent with homoplastic DMME evolution in the marsupial and placental lineages.
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Project description:snRNA-seq of opossum (Monodelphis domestica) adult testis
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Project description:Single-cell RNA sequencing of Monodelphis domestica preimplantation embryos
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Project description:Among animal species, cell types vary greatly in terms of number and kind. The broad range of number of cell types among species suggests that cell type origination is a significant source of evolutionary novelty. The molecular mechanisms giving rise to novel cell types, however, are poorly understood. Here we show that a novel cell type of eutherians mammals, the decidual stromal cell (DSC), evolved by rewiring an ancestral cellular stress response. We isolated the precursor cell type of DSCs, endometrial stromal fibroblasts (ESFs), from the opossum Monodelphis domestica. We show that, in opossum ESF, the majority of decidual core regulatory genes respond to decidualizing signals, but do not regulate decidual effector genes. Rather, in opossum ESF, decidual transcription factors function in apoptotic and oxidative stress response. We propose that the rewiring of cellular stress responses could be a general mechanism for the evolution of novel cell types.
2018-06-21 | GSE109309 | GEO
Project description:Evidence from a few genes of diverse species suggests that marsupial X-chromosome inactivation (XCI) is characterized by exclusive, but leaky, inactivation of the paternally derived X chromosome. To comprehensively study the mechanism of marsupial XCI, we profiled parent-of-origin-specific-allele expression, DNA methylation, and histone modifications in opossum fetal brain and extra-embryonic membranes. The majority (152/176) of X-linked genes exhibited paternally imprinted expression with nearly 100% maternal allele expression, whereas 24 loci (14%) escaped inactivation showing varying levels of biallelic expression. In addition to regulation by the non-coding RSX transcript, strong depletion of H3K27me3 at escaper gene loci indicates that histone states also influence opossum XCI. Notably, the opossum does not show an association between X-linked gene expression and promoter DNA methylation. Our study provides the first comprehensive catalogue of parent-of-origin expression status for X-linked genes in a marsupial and sheds light on the regulation and evolution of imprinted XCI in mammals. Profiling of expression level and allele-specific expression ratios in embryonic day 13 opossum (Monodelphis domestica) fetal brain and extra-embyonic membranes by Illumina RNA-seq
2013-09-23 | E-GEOD-45211 | biostudies-arrayexpress
Project description:Monodelphis domestica Whole Genome Sequencing Project
| PRJNA74623 | ENA
Project description:Mammalian spermatogenesis is a highly stereotyped and conserved developmental process that is essential for fitness. At the same time, gene expression in spermatogenic cells is rapidly evolving. This combination of features has been suggested to drive rapid fixation of new gene expression patterns. Using a high-resolution dataset comprising bulk and single-cell data from juvenile and adult testes of the opossum Monodelphis domestica, a model marsupial, we define the developmental timing of the spermatogenic ‘first wave’ in opossum and delineate conserved and divergent gene expression programs across the placental-marsupial split by comparison to equivalent data from mouse, a model placental mammal. Epigenomic data confirmed divergent regulation at the level of transcription, and comparison to data from four additional amniote species identified hundreds of genes with evidence of rapid fixation of expression. This gene set encompasses known and previously undescribed regulators of spermatogenic development.
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