Dissecting the root-fungal interface in 3D reveals spatial-distinct signalling landscapes
This submission comprises all raw sequencing reads generated and/or utilised in the analyses presented in the associated manuscript. The dataset comprises two independent experimental datasets, each designed to address distinct biological questions regarding the transcriptional behaviour of Fusarium oxysporum f. sp. lycopersici (Fol) under varying physiological and conditions of host-interaction.  Experiment 1:   Raw reads from Fusarium oxysporum f. sp. lycopersici (Fol) grown under four distinct nutrient and substrate conditions: minimal-media broth (Fol-Min-Media), granular microjammed (Gamborg's B5 Microjammed Granular hydrogel), monolithic agarose (Gamborg's B5 in conventional homogeneous agarose), and broth (Gamborg's B5 in liquid). This design enables dissection of transcriptional responses attributable to nutritional composition and substrate mechanical architecture.    Experiment 2   Raw reads from a Microjammed Granular hydrogel-based tomato root–Fol infection system. Samples were collected at 12, 24, and 36 hours post-inoculation (hpi). At 12 hpi, tomato root, tip and fungal samples ex-planta surrounding the root surface were profiled. At 24 hpi, tomato root samples and spatially stratified fungal samples collected from ex-planta at the root-proximal and root-distal zones were profiled to characterise host-induced transcriptional rewiring in Fol in proximity to the root surface when the fungus is approaching a host plant before the physical contact. At 36 hpi, only tomato root/tip samples were collected to capture the plant transcriptional responses to infection after establishment of the fungal compatibility within the root.
This submission comprises all raw sequencing reads generated and/or utilised in the analyses presented in the associated manuscript. The dataset comprises two independent experimental datasets, each designed to address distinct biological questions regarding the transcriptional behaviour of Fusarium oxysporum f. sp. lycopersici (Fol) under varying physiological and conditions of host-interaction.  Experiment 1:   Raw reads from Fusarium oxysporum f. sp. lycopersici (Fol) grown under four distinct nutrient and substrate conditions: minimal-media broth (Fol-Min-Media), granular microjammed (Gamborg's B5 Microjammed Granular hydrogel), monolithic agarose (Gamborg's B5 in conventional homogeneous agarose), and broth (Gamborg's B5 in liquid). This design enables dissection of transcriptional responses attributable to nutritional composition and substrate mechanical architecture.    Experiment 2   Raw reads from a Microjammed Granular hydrogel-based tomato root–Fol infection system. Samples were collected at 12, 24, and 36 hours post-inoculation (hpi). At 12 hpi, tomato root, tip and fungal samples ex-planta surrounding the root surface were profiled. At 24 hpi, tomato root samples and spatially stratified fungal samples collected from ex-planta at the root-proximal and root-distal zones were profiled to characterise host-induced transcriptional rewiring in Fol in proximity to the root surface when the fungus is approaching a host plant before the physical contact. At 36 hpi, only tomato root/tip samples were collected to capture the plant transcriptional responses to infection after establishment of the fungal compatibility within the root.