biostudies-arrayexpressAmey RedkarFusarium oxysporumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17442This 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.biostudies-arrayexpressGrowth Protocol - For comparing growth across different conditions, the fungi were grown in Potato Dextrose Broth (HiMedia, MB000) or Gmaborg media as prescribed in the manuscript by inoculating from a glycerol culture. The cultures were then incubated for 72 hours at 28°C and 140 rpm. For the infection, Fol and tomato seedlings were grown in Gamborg jammed granular microgel matrix on petridish. For infection, seedlings were placed in Gamborg jammed granular microgel matrix containing fungal spores.Nucleic Acid Extraction - RNA was extracted from snap-frozen recovered jammed granular microgel matrix samples and/or tomato roots at defined time points using RNA extraction was performed using Qiagen RNeasy Kit for RNA Purification, using 100 mg tissue/gel and 500 µL of lysis buffer (washing and elution were done as per the manufacturer’s guidelines). RNA was eluted in 40 µL nuclease water, followed by DNase treatment.Sample Collection - Samples were collected at specified time points by either recovering the fungus from the jammed granular microgel matrix or by harvesting the mycelia through a cheese cloth when grown in liquid cultures. Collected samples were immediately frozen in liquid nitrogen. Plant roots were chopped and frozen in liquid nitrogen.Sequencing - The library was sequenced on the NovaSeq 6000 platform using SP flowcell with 2x100 bp paired end reads.Library Construction - The library was prepared using NEBNext Ultra™ II Directional RNA Library Prep with sample purification beads.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Plant rhizospheric interactions represent intricate relationships that determine plant fitness and are crucial for interrogating host-pathogen dynamics, with significant fundamental and translational implications. Most fungal-plant interactions occur in soil – a disordered and granular 3D environment – and hence remain challenging to unravel due to complex regulatory networks. Our current body of evidence characterizing these molecular dialogues largely stems from experimental systems employing soil or in vitro 2D flat plates, hydroponics and gnotobiotic systems. Soil itself features widely varying visco-elasto-plastic material properties, and its inherent opacity precludes direct visualization of the infection progression in complex diseases such as wilts and root rots. Here, we introduce the first such optically transparent, 3D granular growth matrix to recapitulate complex properties of the soil microenvironment, which enables direct, cellular-level visualization of the plant-fungal interface. Our mechanically tunable 3D matrices support long-term co-culture of plants and fungi with compatibility to classical molecular and physiological assays for unravelling the early signalling events and inter-kingdom crosstalk. By leveraging the optical transparency of this matrix, we track fungal development in response to host signals ex-planta with 3D resolution, to report pioneering evidence of hyphal reprogramming preferentially towards the root tips during the early stages of infection. Crucially, we integrate spatiotemporal transcriptomic analyses and discover distinct pathogen-host ex- and in-planta modules during early signalling, which are likely associated with biomimetic soil-like environments. Together, our findings establish an integrable and versatile 3D platform offering an unprecedented view of the pathogen infection processes, which enables fundamental discoveries into the biological regulation of growth and infection. These insights hold immense potential for advancing our understanding of host immune responses and adaptation of filamentous pathogens, as well as open avenues to decipher drought and disease-resistance mechanisms with major agricultural benefits.RNA-seq of coding RNAFusarium oxysporumDissecting the root-fungal interface in 3D reveals spatial-distinct signalling landscapesSyona Baptista Thomas, M Sreepadmanabh, Vidha Srivastava, Abhirami Puzhakkal, Tapomoy Bhattacharjee, Amey RedkarAmey RedkarfalseDissecting the root-fungal interface in 3D reveals spatial-distinct signalling landscapesThis 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.2026-08-14T00:00:00Z2026-08-14T01:00:45.606Z2026-08-04T09:20:33.767ZE-MTAB-17442ERP203272EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_000418410.1101/2025.10.22.683817