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Nematode metagenome

ABSTRACT: nematode metagenome Raw sequence reads

PROVIDER: PRJNA609008 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR11192300_1.fastq.gz	Fastqsanger.gz
	SRR11192300_2.fastq.gz	Fastqsanger.gz
	SRR11192400_1.fastq.gz	Fastqsanger.gz
	SRR11192400_2.fastq.gz	Fastqsanger.gz
	SRR11192500_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing analysis to examine the transcriptional responses of the nematode-trapping fungus Duddingtonia flagrans with the treatment of extraction of Caenorhabditis elegans

Project description:Purpose: To identify the putative high pathogenicity for fungal infection of nematodes of the nematode-trapping fungus Duddingtonia flagrans, RNA-seq was used to examine the transcriptional responses in three stages with the treatment of extraction of Caenorhabditis elegans. Methods:mRNA of three interaction stages (0h, 12h, 48h) were generated by deep sequencing, in triplicate, using Illumina Hiseq platforme,and 125 bp paired-end reads were generated.Then raw reads were firstly processed by in-house perl scripts and clean reads were obtained by removing reads containing adapter,poly-N and low quality reads. Clean reads were aligned to the reference genome using TopHat V2.0.12 (Duddingtonia flagrans genome with the accession number of MDKD00000000).Then HTSeq and DESeq were used to analyse the gene expression level. Results: After sequencing, 81.8% of the genes predicted in genome of Duddingtonia flagrans were expressed (FPKM>1) in the samples free of treatment of extraction of Caenorhabditis elegans (0h). After treatment with nematode extracts for 12 h , 40.7% of predicted genes, including 1,752 up-regulated genes and 2,072 down-regulated genes, were found to be differentially expressed (padj<0.05, DESeq) compared to the genes at 0 h. Similarly, after treatment with nematode extracts for 48 h, 13.8% of predicted genes, including 673 up-regulated genes and 628 down-regulated genes, were found to be differentially expressed compared to the genes at 12 h.

2019-11-14 | GSE95525 | GEO

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