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ABSTRACT: Monodelphis domestica whole genome sequencing

PROVIDER: PRJNA819000 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18452360_1.fastq.gz	Fastqsanger.gz
	SRR18452360_2.fastq.gz	Fastqsanger.gz
	SRR18452361_1.fastq.gz	Fastqsanger.gz
	SRR18452361_2.fastq.gz	Fastqsanger.gz

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The Transcriptome of the Didelphys virginiana Opossum Kidney OK Proximal Tubule Cell Line

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.

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Ab initio identification of a marsupial-specific imprinted gene via genome-wide histone state profiling in opossum fibroblasts

Project description:We generated genome-wide histone maps of four histone modifications, H3K4me3, H3K9Ac, H3K9me3, and H3K27me3, by ChIP-seq in male fibroblasts isolated from a model marsupial, Monodelphis domestica. We assayed the correlation and association of these histone modifications with each other, certain genomic elements such as CpG islands and predicted promoters, and the transcriptional states of the genes they mark. Generally, we found that promoters of actively transcribed genes are associated with H3K4me3 and H3K9Ac and lack H3K9me3 and H3K27me3. We also show that transcriptionally opposing, mutually exclusive histone modifications mark monoallelically expressed and imprinted genes in our samples.

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