12_Infection_Fungus_1
Protocols: 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.   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.  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. The library was prepared using NEBNext Ultra™ II Directional RNA Library Prep with sample purification beads.
ENA first public
2026-08-14
INSDC center name
National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR)
INSDC status
public
Submitter Id
E-MTAB-17442:12_Infection_Fungus_1
broker name
ArrayExpress
collection date
not collected
genotype
Fusarium oxysporum f. sp. lycopersici 4287
geographic location (country and/or sea)
not collected
growth condition
Gamborg B5
isolate
not applicable
organism part
Fungal mycelia
sample name
E-MTAB-17442:12_Infection_Fungus_1
scientific_name
Fusarium oxysporum
stimulus
Fungus near plant root at 12 HPI