{"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-15092"],"description":["RNA was extracted from axenically grown Fo47 and Fol cultures and Marchantia polymorpha Tak1 thalli infected with these strains at 3DPI. There are 3 biological replicates in each set. Sequencing was carried out using NovaSeq 6000 platform using SP flowcell with 2x100bp sequencing read length."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The extracted RNA  was eluted in 40 μL nuclease-free water and quantified using Qubit and quality assessment was performed on Agilent TapeStation. From the total RNA, mRNA was enriched using NEBNext Poly(A) mRNA magnetic isolation Module. The library was prepared using NEBNext Ultra™ II Directional RNA Library Prep with sample purification beads.","Nucleic Acid Extraction - After crushing the tissue in liquid nitrogen, RNA was extracted using Qiagen RNeasy Kit using 100 mg tissue 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.","Sequencing - Sequencing was performed on the NovaSeq 6000 platform, using SP flowcell with 2x100bp sequencing read length.","Sample Collection - Infected thalli were collected and snap-frozen in liquid nitrogen.","Growth Protocol - Gemmae from the Mp Tak-1 were plated on Gamborg B5 media without sucrose, solidified with 1.5% agar, and maintained at 22°C under a 20:4-hour day-night photoperiod. For infection, 21-day-old thalli (≥ nine thalli per treatment) were dipped in microconidial suspension for 20 mins. Dipping in water was performed as a mock/control treatment. After air drying for 15 minutes, the infected thalli were incubated at 28°C with a 20:4-hour day-night cycle and samples were harvested at the defined time points.   Fo isolates were grown in Potato Dextrose Broth (PDB) for 72 hours at 28°C and 140 rpm. Microconidia were harvested by filtering fungal cultures through the cheese cloth. The spores were pelleted by centrifugation and resuspended in sterile water.Spore suspension for infection was created by diluting the spore suspension to a final concentration of 10^5 spores/mL.."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Fusarium oxysporum"],"pubmed_title":["Transcriptional plasticity of fast core chromosomes governs establishment of a fungal pathogen on evolutionarily distant plant lineages"],"pubmed_authors":["Vidha Srivastava, Siddharth Kaushik L S, Naga Jyothi Pullagurla, Bernd Zechmann, Antonio Di Pietro, Debabrata Laha, Amey Redkar","Amey Redkar"],"additional_accession":[]},"is_claimable":false,"name":"RNA sequencing for axenically grown Fol and Fo47 fungal cultures as well as Marchantia polymorpha Tak1 thalli infected with these strains","description":"RNA was extracted from axenically grown Fo47 and Fol cultures and Marchantia polymorpha Tak1 thalli infected with these strains at 3DPI. There are 3 biological replicates in each set. Sequencing was carried out using NovaSeq 6000 platform using SP flowcell with 2x100bp sequencing read length.","dates":{"release":"2026-05-04T00:00:00Z","modification":"2026-05-04T01:03:01.419Z","creation":"2025-04-25T10:52:09.003Z"},"accession":"E-MTAB-15092","cross_references":{"ENA":["ERP171970"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184"],"doi":["10.1101/2025.03.27.645276"]}}