This readme file was generated on [2024-09-20] by [Laura Riggi] and provides a list and description of each file included in the dataset. ----------------------------------------- DATASET GENERAL INFORMATION ----------------------------------------- Title of dataset: Data for: Strip-cropping legacy enhances potato plant defence responses to aphids via soil-mediated mechanisms Creator(s)/Primary investigator(s): [Laura Riggi] ----------------------------------------- FILES OVERVIEW ----------------------------------------- [Experimental data] [This file contains the explanation for the exprimental data collected in the green-house. This includes data on yield, plant biomass, plant N & P, AMF colonization, aphid count] [Metabolome data] [This file contains the explanation for the raw metabolomic plant data collected and analysed using LC-MS. This variables refrs to several data files: Matabolome data_Samples (gives information on samples treatments); Metabolome data (gives information on the LC-MS raw data per sample);Metabolome_Putative annotations (gives information on the raw annotation based on clusters);Metabolome_KNAPSACK matches M-H (gives information on compounds annotation from the online KNAPSACK database with M-H); Metabolome_KNAPSACK matches M+FA-H (gives information on compounds annotation from the online KNAPSACK database with M+FA-H ] ----------------------------------------- DATA-SPECIFIC INFORMATION FOR [Experimental data] ----------------------------------------- Number of columns/variables: 18 Number of rows/cases: 121 Explanation of missing/empty data : empty cells are N/A Variable list: [sample_id]:[individual sample id per pot] [block]:[block in the green house] [Soil_treatment]:[experimental treatment, soil diversity treatment with two levels (MC: mono-cropping and SC: strip-cropping)] [AMF_treatment]:[experimental treatment, AMF inoculation with three levels (AMF+: AMF inoculated, AMF0: no AMF inoculation, AMF-: AMF reduced using soil core). Note AMF- was not included in the published manuscrip and anlyses as the treatment did not work] [Herbivore_treatment]:[experimental treatment, Herbivore treatment with two levels (H0: no aphid inoculation, H: aphid inoculation)] [aphid_count_on_plant]:[Count of aphids on infested plant at harvest] [N]:[Shoot Nitrogen (mmol/kg)] [P]:[Shoot Phosphorous (mmol/kg)] [rootDW]:[Belowground, root dry weight (g)] [shootDW]:[Aboveground, shoot dry weight (g)] [tuber_original]:[planted tuber weight (g)] [harvest_tuber]:[harvested tubers weight (g)] [harvest_tubers#]:[number of harvested tubers] [harvest_tuber_mean_weight]:[harvested tuber individual mean weight] [AMFobs]:[AMF observations] [AMFtot]:[AMF structures observed (includes hyphea, arbuscules and vesicles)] [Dim.1_PCA]:[PCA coordiates axis 1 from the metabolomic data (see published manuscript)] [Dim.2_PCA]:[PCA coordiates axis 2 from the metabolomic data (see published manuscript)] ----------------------------------------- DATA-SPECIFIC INFORMATION FOR [Metabolome data] ----------------------------------------- Explanation of missing/empty data : empty cells are N/A Variable list: [Adduct]:[ion type] [AMF_treatment]:[experimental treatment, AMF inoculation wuth three levels (AMF+: AMF inoculated, AMF0: no AMF inoculation, AMF-: AMF reduced using soil core). Note AMF- was not included in the manuscript and analyses as the treatment did not work] [CAS]:[compound code Chemical Abstract Service] [cluster_identified_by_LMMs]:[compounds that have been selected using the LMMs methods (see manuscript)] [cluster_identified_by_RF]:[compounds that have been selected using the Random Forest methods (see manuscript)] [clusterId]:[unique cluster id number] [comments]:[comments from authors] [compound_ID]:[name in KNApSAcK] [Elemental_formula]:[molecular formula] [F0XXXXX]:[unique LC-MS file id (refered to as metabolome_id)] [Herbivore_treatment]:[experimental treatment, Herbiore treatment with two levels (H0: no aphid inoculation, H: aphid inoculation)] [ID_manually]:[manually identified] [identifier]:[identifier ion] [Inchi_code]:[International Chemical Identifier code] [KnapSack_ID]:[code KNAPSACK DB assuming [M-H]- as molecular ion; a maximum of 5 hits are provided in "KNAPSACK matches [M-H]" and "KNAPSACK matches [M+FA-H]"] [Mass]:[exact mass of molecule] [mass_list]:[masses (in microdalton) in each cluster] [max_value]:[maximum intensity value in all samples analysed] [metabolome_id]:[unique LC-MS file id] [nr_of_peaks_in_cluster]:[number of mz peaks in cluster conform MSClust tool] [organism]:[organism in which compound is recorded in KNAPSACK DB] [possible_ID]:[putative annotation] [ppm_deviation]:[deviation observed mz versus calculated mz, in parts per million] [put_mol_ion]:[putative molecular ion: most abundant mass in cluster] [QUANT_END]:[column referrring to end of relative level of compound in samples] [QUANT_START]:[column referrring to start relative level of compound in samples] [ref]:[reference] [relative_intensity_list]:[relative intensity of the masses in each cluster] [RT(min)]:[LC retention time in minutes] [sample_id]:[sample code] [Soil_treatment]:[experimental treatment, soil diversity treatment with two levels (MC: mono-cropping and SC: strip-cropping)]