{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Amey Redkar"],"organism":["Fusarium oxysporum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17442"],"description":["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 re"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Plant 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 introduc"],"study_type":["RNA-seq of coding RNA"],"species":["Fusarium oxysporum"],"pubmed_title":["Dissecting the root-fungal interface in 3D reveals spatial-distinct signalling landscapes"],"pubmed_authors":["Syona Baptista Thomas, M Sreepadmanabh, Vidha Srivastava, Abhirami Puzhakkal, Tapomoy Bhattacharjee, Amey Redkar","Amey Redkar"],"additional_accession":[]},"is_claimable":false,"name":"Dissecting the root-fungal interface in 3D reveals spatial-distinct signalling landscapes","description":"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 re","dates":{"release":"2026-08-14T00:00:00Z","modification":"2026-08-14T01:00:45.606Z","creation":"2026-08-04T09:20:33.767Z"},"accession":"E-MTAB-17442","cross_references":{"ENA":["ERP203272"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"],"doi":["10.1101/2025.10.22.683817"]}}