Wheat and Tan Spot Fungus RNA-seq Expression Profiles During Infection

Paula Moolhuijzen generated transcriptional datasets for wheat and the pathogen Pyrenophora tritici-repentis using RNA sequencing. The data includes gene expression measurements for 9,093 to 13,770 pathogen genes and wheat genes at 3 and 4 days post-infection, along with in vitro pathogen growth stages. Files contain sample statistics, expression values in FPKM, log2 fold changes, and effector protein predictions.

Use Cases

• Identify differentially expressed wheat genes during fungal infection based on log2(fold_change) values.
• Predict candidate fungal effector proteins using the provided Effectorp probability scores.
• Compare pathogen gene expression in planta versus in vitro growth conditions using FPKM values.
• Analyze transcriptional changes in the Pyrenophora tritici-repentis isolate M4 over the infection time course.

Strengths

• Includes expression data for a specific pathogen isolate (M4) with 9,093 to 13,770 GenBank accession numbers detailed.
• Provides paired in planta and in vitro pathogen expression data, allowing for comparative analysis.
• Supplementary methodological documentation in a .docx file offers context for data generation.

Limitations

• Row count for the primary expression tables is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred from file descriptions after download.
• Last update date is unknown; freshness unverified.

Provenance

Source

Paula Moolhuijzen via paperswithcode

Collection Method

RNA sequencing of in vitro and in planta samples during wheat tan spot infection.