{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Gregory Franklin"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Hypericum perforatum"],"species":["Hypericum perforatum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15161"],"description":["The study was conducted to understand the defense responses of H. perforatum following co-cultivation with A. tumefaciens and A. rhizogenes through an integrative transcriptomics and metabolomics approach."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated from 100 mg of biomass using the Sigma Spectrum RNA extraction kit (Sigma-Aldrich, USA). RNA samples with an RNA integrity number (RIN) of at least seven were used for RNAseq analysis.","Sample Treatment - A. tumefaciens or A. rhizogenes was added to H. perforatum cell suspension cultures in the exponential phase (three to five days after subculture).","Sequencing - After size selection, the double-stranded cDNA was purified by PCR and 150 bp paired-read Illumina sequencing was performed (Novogene, Beijing, China).","Sample Collection - After co-cultivation of Agrobacteria and A. tumefaciens, the cells were collected at different time points (0.5 h, 3 h, 12 h, 24 h). After the cells were vacuum filtered from the medium, they were immediately cryopreserved in liquid nitrogen and stored at -80 °C.","Growth Protocol - Three biological replicates for the treatment and control were incubated in a growth chamber with a photoperiod of 16 hours of light and 8 hours of darkness at 25 °C, an irradiation of 80 µmol m-²s-¹ and a relative humidity of 70, and both the treated and control cultures were kept alive.","Library Construction - Random hexamer primers were used to synthesise the cDNA after random fragmentation of the mRNA. DNA polymerase I, dNTPs, RNase H and a special second-strand synthesis buffer (Illumina) were used to generate the second strand."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Maria Nuc","Gregory Franklin","Paweł Krajewski","Rajendran K Selvakesavan"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq analysis of cell suspension culture of Hypericum perforatum","description":"The study was conducted to understand the defense responses of H. perforatum following co-cultivation with A. tumefaciens and A. rhizogenes through an integrative transcriptomics and metabolomics approach.","dates":{"release":"2025-09-01T00:00:00Z","modification":"2025-09-01T12:30:16.26Z","creation":"2025-05-21T14:15:48.567Z"},"accession":"E-MTAB-15161","cross_references":{"ENA":["ERP172808"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}