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Series GSE78058 Query DataSets for GSE78058
Status Public on Apr 11, 2016
Title RNA-Seq Analysis of VRF1-dependent Genes in the appressoria of Magnaporthe oryzae 70-15
Organism Pyricularia oryzae 70-15
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to find out the genes regulated directly or indirectly by C2H2 transcription factors Vrf1 by RNA-seq in the rice blast fungus Magnaporthe oryzae
Methods: Appressorial mRNAs of the wild type strain 70-15 and Δvrf1 conidia incubated in H2O on plastic membranes at 28˚C for 5 h, in triplicate independently for each strain, were extracted and isolated by RNeasy Plant mini kit (QIAGEN) and AMPure XP beads (Beckman). RNA-sequencing libraries were constructed using NEBNext RNA sample preparation kit (NEB). Samples were sequenced on Illimina Nextseq500 SE75 (1*75).The M. oryzae genome database (Version 7) (www.broadinstitute.org) was used as a reference gene database. Genome-wide transcript levels of genes were quantified in fragments per kilobase of exon model per million mapped reads (FPKM) (Trapnell 2010). Gene Ontology (GO) enrichment analyses for differentially expressed genes were performed using hypergeometric test with topGO, and p-values were adjusted with Bonferroni for multiple testing (Alexa 2006). And we selected FDR < 0.05 as enrichment terms.
Results and Conclusions: We identified 2709 genes regulated by VRF1 through RNA-Seq, with 1739 genes down-regulated and 970 genes up-regulated in Δvrf1. Interestingly, a lots of appressorium-specific genes were down-regulated in Δvrf1, suggesting that Vrf1 is a specific transcription factor which regultes the expression of genes in appressorium formation.
 
Overall design Appressorial mRNA profiles of the wild type strain 70-15 (WT) and Δvrf1 conidia incubated in H2O on plastic membranes for 5 h were generated, in biologic triplicate.
 
Contributor(s) Lu JP, Cao HJ, Huang PY, Lin FC
Citation(s) 27041000
Submission date Feb 18, 2016
Last update date May 15, 2019
Contact name Jianping Lu
E-mail(s) jplu@zju.edu.cn
Organization name Zhejiang University
Department College of Life Sciences
Street address 866 Yuhantang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
 
Platforms (1)
GPL21479 HiSeq X Ten (Magnaporthe oryzae 70-15)
Samples (6)
GSM2065783 WT rep1
GSM2065784 WT rep2
GSM2065785 WT rep3
Relations
BioProject PRJNA312478
SRA SRP070502

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE78058_RAW.tar 520.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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