NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7051567 Query DataSets for GSM7051567
Status Public on Feb 25, 2023
Title A: XIPO323_6hr_r1
Sample type SRA
 
Source name Triticum aestivum (NCBI:txid4565), Zymoseptoria tritici (NCBI:txid336722)
Organisms Triticum aestivum; Zymoseptoria tritici IPO323
Characteristics tissue: infected leaf
genotype: T. aestivum cv. Riband, Z. tritici IPO323 (NCBI:txid336722)
treatment: 6 hours post infection
Treatment protocol Second leaves of wheat cv. Riband seedlings grown for 21 days in complete compost were inoculated with spores of mutant isolates collected from YPD cultures, which had been washed and re-suspended in dH2O+0.01% Tween 20 to a density of 1x107 spores ml-1
Extracted molecule polyA RNA
Extraction protocol Infected leaf tissues were excised at 6 and 24 h and immediately snap frozen. Each technical and biological replicate incorporated five leaves. Total RNA was isolated using the TRIZOL procedure (Invitrogen) and RNA quality was assessed using Nanodrop and gel electrophoresis.
The library construction protocol was carried out by the contractor Novogen. They report they did the following. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Quality control of reads was performed using MultiQC. Sequence trimming of recognised adaptors was performed using Trimmomatic (Bolger et al., 2014) v0.39-Java-11. Reads were mapped to the Z. tritici IPO323 genome using HiSat2 (Kim et al., 2019) v2.2.1-foss-2019b. Principal Component Analysis (PCA) was performed on sample differences of variance stabilising transformed (vsd) gene count data to confirm that biological replicates clustered together. Count determination was performed using featureCounts (Liao et al., 2014), part of the SubRead package v2.0.0-GCC-8.3.0. Library normalisation and differential expression (DE) calling were done using the Bioconductor package v3.16 DESeq2 (Love et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html) in R.
Assembly: Triticum aestivum Chinese Spring IWGSC v2.1; Zymoseptoria_tritici MYCGR v2.0
Supplementary files format and content: taestivumCellWallRNAStringent.txt tab is delimited plain text listing gene counts generated using SubRead FeatureCounts
 
Submission date Feb 20, 2023
Last update date Feb 25, 2023
Contact name Daniel Smith
E-mail(s) dan.smith@rothamsted.ac.uk
Organization name Rothamsted Research
Department IDE
Street address West Common
City Harpenden
State/province Hertfordshire
ZIP/Postal code AL5 2JQ
Country United Kingdom
 
Platform ID GPL33143
Series (1)
GSE225623 Fungal plant pathogen “mutagenomics” reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor 
Relations
BioSample SAMN33373531
SRA SRX19435349

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap