{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Elia Lacchini"],"organism":["Saponaria officinalis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14773"],"description":["The experiment aims to identify genes encoding enzymes involved in the biosynthesis of triterpenoid saponins in Saponaria officinalis. RNA-seq data generated were generated from leaves, stems, and roots from 3 months old- hydroponically grown S. officinalis plants that were treated with 50 µM methyl jasmonate or a mock control. Samples were collected at 6 and 24 hours post-treatment. A total of 36 RNA samples, each consisting of triplicate biological replicates pooled from three plants, were collected. RNA was extracted using the ReliaPrep RNA miniprep system (Promega), sequenced on an Illumina HiSeq 6000 platform with 100 bp single-end reads, and mapped to the reference transcriptome using Salmon."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Each samples was ground in liquid nitrogen using mortar and pestle. RNA was extracted from leaves, stems and roots sampled in triplicate (each biological replicate being a pool of three individual plants) at 6 and 24 hours after treatment. RNA was extracted from the sampled S. officinalis tissues using the ReliaPrep RNA miniprep Systems (Promega™), following manufacturer’s instructions for fibrous tissues.","Growth Protocol - Seeds of Saponaria officinalis used for transcriptome sequencing were sourced from the seed company Jelitto (https://www.jelitto.com/, Schwarmstedt, Germany). Seeds were surface sterilized and placed in Magenta boxes with germination medium containing: 2.2 gr L-1 MS with vitamins (Duchefa), 1.5% sucrose, 0.1% MES, 0.4% Phytagel, pH was adjusted with 1 M KOH to 5.8. Sealed boxes were kept in the dark for 1 week at 4 degrees prior transferring to long day for germination. Seeds were germinated in long day (18 hours of light) under cold fluorescent lamps at 24 degrees. Two weeks after germination plantlets were transferred to hydroponic boxes containing nutrient solution (1/4 MS with vitamins) and grown in long day (18 hours of light) at 24 degrees for three months prior elicitation and sampling.","Sequencing - Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (Single Reads, 100 cycles, 1% PhiX) at the VIB Nucleomics Core (www.nucleomics.be).","Sample Treatment - Elicitation was perfomed by adding Methyl Jasmonate to the nutrient solution to reach a final concentration of 50 uM, mock treated plants were instead administered with the same amount of ethanol added to the hydroponic solution.","Sample Collection - Briefly. 3 months old Saponaria plants were harvested, using a surgical blade roots were separated from shoots and leaves, each tissue was collected separately and snap-frozen in liquid nitrogen prior processing for RNA extraction.","Library Construction - RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-8000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 500 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA Polymerase I and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNAseq datasets were processed using a pipeline implemented on galaxy (https://usegalaxy.eu/). The raw .fastq files were uploaded onto Galaxy.eu, Trimmomatic was used to remove Illumina adapter sequences and low-quality bases. Quality of reads for downstream analysis was assessed using FastQC. Filtered, clean FastQC reads were quantified using SalmonQuant to obtain transcript abundances for each dataset"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Saponaria officinalis"],"pubmed_title":["Engineering Gypsophila elegans hairy root cultures to produce endosomal escape-enhancing saponins"],"pubmed_authors":["Alain Goossens","Elia Lacchini, Tongtong Qu, Tessa Moses, Alexander N Volkov and Alain Goossens","Elia Lacchini"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of Saponaria officinalis tissues (leaves, stems and roots) in response to MOCK or 50 uM Methyl Jasmonate treatment at 6 and 24 hours","description":"The experiment aims to identify genes encoding enzymes involved in the biosynthesis of triterpenoid saponins in Saponaria officinalis. RNA-seq data generated were generated from leaves, stems, and roots from 3 months old- hydroponically grown S. officinalis plants that were treated with 50 µM methyl jasmonate or a mock control. Samples were collected at 6 and 24 hours post-treatment. A total of 36 RNA samples, each consisting of triplicate biological replicates pooled from three plants, were collected. RNA was extracted using the ReliaPrep RNA miniprep system (Promega), sequenced on an Illumina HiSeq 6000 platform with 100 bp single-end reads, and mapped to the reference transcriptome using Salmon.","dates":{"release":"2026-01-15T00:00:00Z","modification":"2026-01-15T02:02:25.42Z","creation":"2025-01-23T13:30:46.455Z"},"accession":"E-MTAB-14773","cross_references":{"ENA":["ERP168598"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}