{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Medicago truncatula"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10787"],"description":["We performed a split-root experiment with nodulated roots of Medicago truncatula (A17 accession) to identify systemic molecular responses induced by the inoculation of the oomycete Aphanomyces euteiches. The root systems of nodulated symbiotic plants were divided into two compartments called the \\\"local root compartment\\\" (treated) and the \\\"systemic root compartment\\\", from which samples were obtained for RNAseq analysis. Nodules and the corresponding denodulated roots, localised in the \\\"systemic compartment\\\", were harvested in inoculated or control (mock-inoculated) plants at the same time-points, after 6 hours, 1-, 3- and 6-days after A. euteiches inoculation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - At first, grinding with mortar and pestle is carried out in liquid nitrogen to homogenise the sample. We took an aliquot of 200mg to extract RNAs using miRNeasy® Mini Kit (Qiagen, Venlo, Netherlands) according to the supplier's recommendations. RNAs concentration were measured using the NANODROP 1000 spectrometer (Thermo-Fisher Scientific, Waltham, Massachusetts, USA), and samples kept at -20°C. RNA integrity quality control was assessed using the BioAnalyser (BioRad Laboratories Inc., Hercules, California, USA). For each RNA extraction, polyadenylated plant mRNA libraries were generated and sequenced.","Library Construction - Library preparation and sequencing were performed at the MGX-Montpellier GenomiX Facilities (Montpellier, France). Libraries for sequencing were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, USA). Library quality was checked using the Standard Sensitivity NGS Kit on the Advanced Analytical Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, California, USA), and concentration optimised, performing a qPCR (Light Cycler 480, Roche, Basel, Switzerland).","Sample Collection - Control and treated samples were collected at different time points (6 hours, 1-, 3- and 6-days) following the Aphanomyces euteiches.  We collected three replicate samples for each time point, and each replicate was a pool of the nodules and denodulated roots of 3 plants.","Sample Treatment - A 50 mL suspension containing  30.000 A. euteiches zoospores /mL, produced in Volvic water as previously described (Djébali et al. MPMI, 2009 - http://dx.doi.org/10.1094/MPMI-22-9-1043),  was applied only onto the local compartment on each inoculated plants that were 44 days old. At the same time, we added 50 mL of Volvic water to mock-inoculated samples (controls).","Growth Protocol - Medicago truncatula Jemalong A17 seeds were scarified, germinated as described in Lambert et al. (Lambert, I. et al. J Exp Bot 2020 - http://dx.doi.org/10.1093/jxb/eraa221). Individual plantlets were transferred into hydroponic culture tanks containing a vigorously aerated HY basal nutrient solution adjusted to 5.8 with KOH and supplemented with 1 mM KNO3. We cut the primary root tips of plantlets to promote branching of the root system. The culture chambers conditions were a light intensity of 250 μmol s−1 m−2 photosynthetically active radiation, relative humidity of 70%, a light/dark cycle of 16h/8h and an ambient temperature of 22°C/20°C. We separated the root systems of 4-week-old plants into two parts. The 3-week-old plants were transferred to a nutrient solution adjusted to pH7 supplemented with KNO3 0.5 mM containing the Sinorhizobium medicae md4 bacteria (107 cfu/ml). Typically, nodules appeared after 4 to 6 days and were functional after two weeks. After inoculation, nutrients solutions without mineral N supplement were renewed every week and adjusted to pH7.  For split-root experiments, the root systems of 5-week-old plants were separated into two parts, each side being installed in a separate compartment filled with the same aerated nutrient solution.","Sequencing - Samples sequencing was realised using the Sequence By Sequencing (SBS) technology on the Illumina HiSeq 2500 using the TruSeq Rapid SBS Kit (Illumina, San Diego, California, USA), in the mode single-read 50nt. Sequencing images were processed using the Illumina HiSeq Control Software (HCS), and base calling performed by using the Real-Time Analysis (RTA) software (Illumina, San Diego, California, USA). We performed sequencing results quality controls using the FastQC free software (Babraham Institute, Cambridge, UK) and the free FastQ Screen open-access software (Babraham Institute, Cambridge, UK) to test for possible contaminations."],"figure_sub":["MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["RNA-seq of coding RNA"],"species":["Medicago truncatula"],"additional_accession":["E-MTAB-10786","ERP130718"],"pubmed_authors":["Florian Frugier","Marc Lepetit","Christophe Jacquet","Jonathan Lapleau","Ilana Lambert","Marjorie Pervent","Maxime Bonhomme","Marie-Laure Martin-Magniette","Stefano Colella"]},"is_claimable":false,"name":"Systemic responses induced by  Aphanomyces euteiches inoculation in Medicago truncatula mature nodules or denodulated roots","description":"We performed a split-root experiment with nodulated roots of Medicago truncatula (A17 accession) to identify systemic molecular responses induced by the inoculation of the oomycete Aphanomyces euteiches. The root systems of nodulated symbiotic plants were divided into two compartments called the \\\"local root compartment\\\" (treated) and the \\\"systemic root compartment\\\", from which samples were obtained for RNAseq analysis. Nodules and the corresponding denodulated roots, localised in the \\\"systemic compartment\\\", were harvested in inoculated or control (mock-inoculated) plants at the same time-points, after 6 hours, 1-, 3- and 6-days after A. euteiches inoculation.","dates":{"release":"2026-03-30T00:00:00Z","modification":"2026-03-30T01:03:32.463Z","creation":"2022-03-04T14:46:37.522Z"},"accession":"E-MTAB-10787","cross_references":{"ENA":["ERP130718"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}