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.

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DATASET GENERAL INFORMATION
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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]

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FILES OVERVIEW
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[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 ]

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DATA-SPECIFIC INFORMATION FOR [Experimental data]
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Number of columns/variables: 18

Number of rows/cases: 121

Explanation of missing/empty data <e.g. N/A, null>: 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)]

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DATA-SPECIFIC INFORMATION FOR [Metabolome data]
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Explanation of missing/empty data <e.g. N/A, null>: 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)]
