PRJNA277884 - Roots (P. cinnamomi)

Summary
Resource Type
Analysis
Name
PRJNA277884 - Roots (P. cinnamomi)
Description

"The transcriptome analysis of Q. suber directed to genes related to biotic stress caused by Phytophthora cinnamomi infection, the main biotic contributor to the decline disease aims at the characterization of target and regulatory genes that are responsive to the infectious process leading to the understanding of the genetic mechanisms underlying Quercus defence against P. cinnamomi and is an essential prerequisite for the implementation of future control strategies."

FASTQ files were obtained from the NCBI database using the SRAtoolkit-2.9.4. Tags were removed using TagCleaner-0.16 and high quality reads were filtered using Trimmomatic-0.38. Mapping to the reference genome of Q.suber (NCBI Sequence Read Archive SRP111728 (2017)) was performed using Gmap-2018-07-04 and gene expression in TPM (transcripts per million) was calculated using the counts obtained from featureCounts included in SubRead-v1.6.3.

Program, Pipeline, Workflow or Method Name
PRJNA277884 - Roots (P. cinnamomi)
Program Version
Gmap-2018-07-04, SRAtoolkit-2.9.4, SubRead-v1.6.3, TagCleaner-0.16, Trimmomatic-0.38
Date Performed
Wednesday, April 10, 2019 - 10:07
Data Source
BioSamples
NameTissueTreatmentDescription
SRS872360Tap rootInfection with Phytophtora cinnamomi zoosporesThis biomaterial: SRS872360, was created for the analysis: PRJNA277884 - Roots (P. cinnamomi)
SRS872381RootsInfection with Phytophtora cinnamomi (Control)This biomaterial: SRS872381, was created for the analysis: PRJNA277884 - Roots (P. cinnamomi)
SRS872382RootsInfection with Phytophtora cinnamomiThis biomaterial: SRS872382, was created for the analysis: PRJNA277884 - Roots (P. cinnamomi)
SRS872225Tap rootInfection with Phytophtora cinnamomi zoospores (Control)This biomaterial: SRS872225, was created for the analysis: PRJNA277884 - Roots (P. cinnamomi)