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MeDIP-seq of two phytophthora species at mycelium stage

ABSTRACT: MeDIP-seq of two phytophthora species at mycelium stage

PROVIDER: PRJNA477000 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7405240_1.fastq.gz	Fastqsanger.gz
	SRR7405240_2.fastq.gz	Fastqsanger.gz
	SRR7405241_1.fastq.gz	Fastqsanger.gz
	SRR7405241_2.fastq.gz	Fastqsanger.gz
	SRR7405232_1.fastq.gz	Fastqsanger.gz

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MeDIP-seq of two phytophthora species at mycelium stage

Project description:We report the 6mA methylation profiling in two Phytophthora species and one psdamt3 mutant. Genomic DNA of Phytophthora sojae P6497 mycelium (3-days old), Phytophthora infestans T30-4 mycelium and psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was extracted and sonicated to 200-400bp using Biorupter UCD-600. The antibody sysy 202003 was used to immunoprecipitation. We find that 6mA is associated with lowly expressed genes in two Phytophthora species. 6mA methylome is preferentially associated with TEs, the genes and intergenic regions that form the gene-sparse compartments of Phytophthora genomes. In the psdamt3 mutant, 6mA level reduced in TEs and illustrates the uneven reduction pattern around the TSS.

2018-09-29 | GSE116089 | GEO

Transcriptomes of two phytophthora species at mycelium stage

Project description:Purpose and methods:Transcriptome profiling of Phytophthora sojae P6497 mycelium (3-days old) and Phytophthora infestans T30-4 mycelium (6-days old) were generated to find out the relationship between 6mA methylation and gene expression. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiling of P. sojae psdamt3 mutant T9 (lost 374bp by CRISPR/Cas9) was generated to check the differential expressed genes (DEGs) between the mutant and wild-type P. sojae P6497. Read counts was calculated using featureCounts, and DEGs was calculated using DEseq2 with |log2FC|≥1, y-axis is FDR<0.05. Conclusions: 6mA is associated with lowly expressed genes. Examination of differentially expressed genes (DEGs) in psdamt3 uncovers a total of 3156 genes, with 1544 genes up-regulated and 1622 genes down-regulated.

2018-09-29 | GSE116090 | GEO

Transcriptomes of two phytophthora species at mycelium stage

Project description:Transcriptomes of two phytophthora species at mycelium stage

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H3K27me3 in Phytophthora sojae P6497 and its pssu(z)12 mutant at mycelium stage

Project description:We report the H3K27me3 profile on Avr1b locus in two Phytophthora sojae strains P6497 and pssu(z)12 mutant. Nuclei of Phytophthora sojae P6497 and pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) was extracted and digested to 200-400bp using micrococcal nuclease (MNase: NEB M0247S). The antibody Millipore 07-449 was used to immunoprecipitation. We find significant accumulation of H3K27me3 at Avr1b locus in Avr1b silencing strain P6497 and clear H3K27me3 depletion at Avr1b locus in Avr1b unsilenced strain pssu(z)12 mutant T34.

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Transcriptomes of pssu(z)12 mutant from phytophthora sojae P6497 at mycelium stage

Project description:Purpose and methods:Transcriptome profiling of Phytophthora sojae pssu(z)12 mutant T34 (lost 561bp by CRISPR/Cas9) mycelium (3-days old) were generated to find out the relationship between H3K27me3 and gene expression on Avr1b locus. Wild-type P. sojae P6497 was took as a comparative control. RNA-seq data was mapped using Tophat2, and gene expression data was generated by Cufflinks. Transcriptome profiles were displayed using IGV browser.

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Transcriptomes of pssu(z)12 mutant from phytophthora sojae P6497 at mycelium stage

Project description:Transcriptomes of pssu(z)12 mutant from phytophthora sojae P6497 at mycelium stage

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Chromatin dynamics of Phytophthora during host infection [RNA-seq]

Project description:Dynamic regulation of silencing histone marks, specifically H3K9me3 and H3K27me3, provide effector gene expression plasticity, which enables adaptative responses to environmental fluctuations in plant fungal pathogens. It remains an unanswered question whether the epigenetic regulatory mechanisms governing gene expression during infection stages in Phytophthora are the same as in fungal pathogens. We performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) of three histone modifications, H3K4me3, H3K36me3, and H3K27me3 in P. sojae and P. infestans, encompassing both the mycelium stage, and infection stages (12h post-inoculation (hpi), and 24hpi in soybean, as well as 3dpi in potato respectively).Integrative analysis of ChIP-seq and RNA-seq data of mycelium and infection stages was performed.Overall, our work provides a comprehensive and detailed view of distinctive chromatin dynamic patterns during the infection stages of Phytophthora.

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H3K27me3 in Phytophthora sojae P6497 and its pssu(z)12 mutant at mycelium stage

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ATAC-seq of Phytophthora infestans T30-4 mycelium

Project description:ATAC-seq of Phytophthora infestans T30-4 mycelium

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