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Accession: PRJNA476999 ID: 476999

Transcriptomes of two phytophthora species at mycelium stage

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. Overall design: mRNA profiles of Phytophthora sojae P6497 mycelium (WT,3-days old),PsDAMT3 mycelium(mu,3-days old)and Phytophthora infestans T30-4 mycelium (6-days old) were generated by deep sequencing, in two or three replicates.
AccessionPRJNA476999; GEO: GSE116090
Data TypeTranscriptome or Gene expression
ScopeMultispecies
PublicationsChen H et al., "Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions.", Genome Biol, 2018 Oct 31;19(1):181
SubmissionRegistration date: 20-Jun-2018
The Lab of Pathogenomics, Department of Plant Pathology, Nanjing Agricultural University
RelevanceEnvironmental
Project Data:
Resource NameNumber
of Links
Sequence data
SRA Experiments7
Publications
PubMed1
PMC1
Other datasets
BioSample7
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Supplementary Mbytes13
SRA Data Details
ParameterValue
Data volume, Gbases45
Data volume, Mbytes19428

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