|
Status |
Public on Sep 29, 2018 |
Title |
Transcriptomes of two phytophthora species at mycelium stage |
Organisms |
Phytophthora infestans; Phytophthora sojae |
Experiment type |
Expression profiling by high throughput sequencing
|
Summary |
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.
|
|
|
Contributor(s) |
Dong S, Chen H, Shu H |
Citation(s) |
30382931 |
|
Submission date |
Jun 20, 2018 |
Last update date |
Nov 18, 2018 |
Contact name |
Haidong Shu |
E-mail(s) |
2018202004@njau.edu.cn
|
Organization name |
Nanjing Agricultural University
|
Department |
Department of Plant Pathology
|
Lab |
The Lab of Pathogenomics
|
Street address |
Weigang NO.1
|
City |
Nanjing |
State/province |
Jiangsu |
ZIP/Postal code |
210095 |
Country |
China |
|
|
Platforms (2) |
GPL25217 |
Illumina HiSeq 4000 (Phytophthora sojae) |
GPL25218 |
Illumina HiSeq 4000 (Phytophthora infestans) |
|
Samples (7)
|
|
Relations |
BioProject |
PRJNA476999 |
SRA |
SRP151012 |