Primer sequences of the microcosm genes analysed by real-time RT-PCR. (XLSX 18 kb

Alberto Pellegrini (3436997)

Gerardo Puopolo (3423467)

Ilaria Pertot (658291)

Lieven Sterck (83182)

Luisa Lenzi (3437003)

Michele Perazzolli (83163)

NoemĂ­ Herrero (3437000)

Yves Van de Peer (3785)

Metabolic pathways of the simplified soil microcosm, modulated by incubation in the soil matrix. Metabolic pathways deactivated (left panels) and activated (right panels) by 24Â h incubation in the soil matrix (A) without reinforced modulation (cluster 1) and (B) with reinforced modulation (cluster 15) in the presence of Armillaria mellea and Trichoderma atroviride combined. Metabolic pathways modulated by the introduction of (C) T. atroviride (cluster 3), (D) A. mellea (cluster 5), or (E) both (cluster 7). KEGG pathways were visualised using the iPath2 tool [48], the pathways of upregulated (green) and downregulated (red) genes were highlighted, and a section of the most relevant pathways is reported for each panel. (PDF 2815 kb

The Francis Crick Institute

Additional file 10: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Concentration of the soil microorganism in the simplified soil microcosm. (DOCX 18 kb

Additional file 1: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Additional file 2: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Pearsonâs correlation coefficients among replicates and conditions for RNA-Seq analysis. (PDF 6 kb

Additional file 6: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Biological networks of Gene Ontology (GO) terms. GO biological process terms of the simplified soil microcosm, upregulated by incubation in the soil matrix with similar expression profiles in the presence or absence of Armillaria mellea and Trichoderma atroviride (cluster 1). Significantly enriched GO terms (Pâ<â0.001) were identified using the BiNGO tool [42] and visualised with Cytoscape software [43]. The colour scale legend indicates the level of significance for enriched GO terms. White nodes indicate not significantly overrepresented categories. (PDF 111 kb

Additional file 11: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

Clustering and functional annotation results of differentially expressed genes. (XLSX 15048 kb

Additional file 7: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

https://figshare.com/articles/Additional_file_1_of_Transcriptomic_responses_of_a_simplified_soil_microcosm_to_a_plant_pathogen_and_its_biocontrol_agent_reveal_a_complex_reaction_to_harsh_habitat/4344572

Additional file 2: of Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat

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The Francis Crick Institute

The Francis Crick Institute

The Francis Crick Institute

The Francis Crick Institute

The Francis Crick Institute

The Francis Crick Institute