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Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

ABSTRACT: Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

PROVIDER: PRJNA768481 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18936812.fastq.gz	Fastqsanger.gz
	SRR18936813.fastq.gz	Fastqsanger.gz
	SRR18936814.fastq.gz	Fastqsanger.gz
	SRR18936815.fastq.gz	Fastqsanger.gz
	SRR18936816.fastq.gz	Fastqsanger.gz

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Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

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Project description:An allele of a gene can be epigenetically regulated to show a parent-of-origin biasedexpression pattern, a phenomenon referring to as genomic imprinting. Genomic imprinting ishighly tissue-specific, and mammalian brains are hotspots for this effect. Social behaviourdefects in human and various behavioural changes in mouse, had been linked toinappropriate imprinting, but little is known about how and why such effects occur.The olfactory system in the brain is the essential sensory circuitry that mediates rodent innatebehaviour. Meanwhile, monoallelic expression, a related process, is used extensively inchemosensory neurons to regulate olfactory and vomeronasal receptor choice. We have datashowing receptor gene choice is not a random process, which implies allele choice may bebiased also. The olfactory system is therefore a promising target for detecting allelicimbalance, or even novel imprinting genes, by high-resolution RNA-sequencing followed byallelic-specific transcriptomic mapping.This project is designed to detect parent-of-origin and strain-of-origin allelic expression bias inneurons from two olfactory tissues: main olfactory epithelium (MOE) and olfaction bulb (OB). RNA from reciprocally crossed F1 hybrid mice (S-cross and M-cross) from two distinct inbred strains (C57BL/6J and CAST) have been extracted respectively (two crosses, two tissue types). After sequencing,expression levels from each allele will be distinguished by incorporating SNP and indeldifferences to the strain-specific reference genomes. Analysis will be carried out incollaboration with Gary Churchill's team at the Jackson Laboratory (who have developed amethod of analysing RNAseq data from CAST x C57BL/6J F1s).Genes with strong, reproducible allelic imbalances will be followed up to assess the functional consequences.

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