 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 25, 2023 |
| Title |
F: Y4124_6hr_r3 |
| 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 mutant 4-124 (NCBI:SAMN33272755)
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 |
SAMN33373526 |
| SRA |
SRX19435354 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
