{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001896","ANALYSIS_ID":"AN003077","VERSION":"1","CREATED_ON":"July 20, 2021, 9:07 am"},

"PROJECT":{"PROJECT_TITLE":"Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome","PROJECT_TYPE":"Using metabolomics to compare species","PROJECT_SUMMARY":"Metabolomics comparison of toxic and non-toxic species of phytoplankton from the genus Alexandrium.This study was carried out using 2 pairwise experiments, A. catenella compared to A. tamarense (Experiment 1) and A. pacificum compared to A. tamarense (Experiment 2).","INSTITUTE":"Georgia Institute of Technology","DEPARTMENT":"School of Biological Sciences, School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Parker H. Petit Institute for Bioengineering and Bioscience","LABORATORY":"Kubanek Lab","LAST_NAME":"Brown","FIRST_NAME":"Emily","ADDRESS":"950 Atlantic Dr Atlanta, GA, 30332, USA","EMAIL":"julia.kubanek@biosci.gatech.edu","PHONE":"404-894-8424","PROJECT_COMMENTS":"This study has 3 parts: 2 NMR (Experiment 1: A. catenella-A. tamarense & Experiment 2: A. pacificum-A. tamarense) and MS","CONTRIBUTORS":"Emily R. Brown, Sam G. Moore, David A. Gaul, and Julia Kubanek"},

"STUDY":{"STUDY_TITLE":"NMR Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome (Experiment 2)","STUDY_TYPE":"1H NMR Metabolomics to compare toxic and non-toxic species","STUDY_SUMMARY":"Metabolomics comparison of toxic and non-toxic species of phytoplankton from the genus Alexandrium.This study was carried out using 2 pairwise experiments, A. catenella compared to A. tamarense (Experiment 1) and A. pacificum compared to A. tamarense (Experiment 2). This study includes the NMR data from Experiment 2.","INSTITUTE":"Georgia Institute of Technology","DEPARTMENT":"School of Biological Sciences, School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Parker H. Petit Institute for Bioengineering and Bioscience","LABORATORY":"Kubanek Lab","LAST_NAME":"Brown","FIRST_NAME":"Emily","ADDRESS":"950 Atlantic Dr Atlanta, Georgia USA 30332","EMAIL":"julia.kubanek@biosci.gatech.edu","PHONE":"404-894-8424","NUM_GROUPS":"2","TOTAL_SUBJECTS":"30","STUDY_COMMENTS":"Part 2 of 3. This part includes NMR analysis of non-polar metabolites from Experiment 2 using oPLSDA. Parts 1 and 3 inlcude NMR analysis of non-polar metabolites from Experiment 1 and the corresponding mass spectrometry metabolomics for both Experiments 1 and 2."},

"SUBJECT":{"SUBJECT_TYPE":"Other organism","SUBJECT_SPECIES":"Alexandrium pacificum; Alexandrium tamarense","TAXONOMY_ID":"1565494; 2926","GENOTYPE_STRAIN":"CCMP 1493; CCMP 2023","GENDER":"Not applicable"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Apacificum 1",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 1","Cells_per_mL":"17947","Number_of_cells_extracted":"4468803","NMR_solvent_volume (uL)":"276","MS_solvent_volume (uL)":"984"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 2",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 2","Cells_per_mL":"17947","Number_of_cells_extracted":"4468803","NMR_solvent_volume (uL)":"276","MS_solvent_volume (uL)":"984"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 3",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 3","Cells_per_mL":"14853","Number_of_cells_extracted":"3698397","NMR_solvent_volume (uL)":"229","MS_solvent_volume (uL)":"814"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 4",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 4","Cells_per_mL":"16957","Number_of_cells_extracted":"4222293","NMR_solvent_volume (uL)":"261","MS_solvent_volume (uL)":"929"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 5",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 5","Cells_per_mL":"15967","Number_of_cells_extracted":"3975783","NMR_solvent_volume (uL)":"246","MS_solvent_volume (uL)":"875"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 6",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"none","Cells_per_mL":"16462","Number_of_cells_extracted":"4099038","NMR_solvent_volume (uL)":"253","MS_solvent_volume (uL)":"902"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 7",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"none","Cells_per_mL":"15224","Number_of_cells_extracted":"3790776","NMR_solvent_volume (uL)":"234","MS_solvent_volume (uL)":"834"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 8",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 8","Cells_per_mL":"16710","Number_of_cells_extracted":"4160790","NMR_solvent_volume (uL)":"257","MS_solvent_volume (uL)":"916"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 9",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 9","Cells_per_mL":"15348","Number_of_cells_extracted":"3821652","NMR_solvent_volume (uL)":"236","MS_solvent_volume (uL)":"841"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 10",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 10","Cells_per_mL":"15348","Number_of_cells_extracted":"3821652","NMR_solvent_volume (uL)":"236","MS_solvent_volume (uL)":"841"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 11",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 11","Cells_per_mL":"18071","Number_of_cells_extracted":"4499679","NMR_solvent_volume (uL)":"278","MS_solvent_volume (uL)":"990"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 12",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 12","Cells_per_mL":"15472","Number_of_cells_extracted":"3852528","NMR_solvent_volume (uL)":"238","MS_solvent_volume (uL)":"848"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 13",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 13","Cells_per_mL":"15224","Number_of_cells_extracted":"3790776","NMR_solvent_volume (uL)":"234","MS_solvent_volume (uL)":"834"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 14",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 14","Cells_per_mL":"14729","Number_of_cells_extracted":"3667521","NMR_solvent_volume (uL)":"227","MS_solvent_volume (uL)":"807"}
},
{
"Subject ID":"-",
"Sample ID":"Apacificum 15",
"Factors":{"Treatment":"Alexandrium_pacificum"},
"Additional sample data":{"RAW_FILE_NAME":"Apacificum 15","Cells_per_mL":"14977","Number_of_cells_extracted":"3729273","NMR_solvent_volume (uL)":"230","MS_solvent_volume (uL)":"821"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 1",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 1","Cells_per_mL":"18319","Number_of_cells_extracted":"4561431","NMR_solvent_volume (uL)":"282","MS_solvent_volume (uL)":"1004"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 2",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 2","Cells_per_mL":"17947","Number_of_cells_extracted":"4468803","NMR_solvent_volume (uL)":"276","MS_solvent_volume (uL)":"984"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 3",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"none","Cells_per_mL":"17947","Number_of_cells_extracted":"4468803","NMR_solvent_volume (uL)":"276","MS_solvent_volume (uL)":"984"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 4",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"none","Cells_per_mL":"17947","Number_of_cells_extracted":"4468803","NMR_solvent_volume (uL)":"276","MS_solvent_volume (uL)":"984"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 5",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 5","Cells_per_mL":"17081","Number_of_cells_extracted":"4253169","NMR_solvent_volume (uL)":"263","MS_solvent_volume (uL)":"936"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 6",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 6","Cells_per_mL":"17576","Number_of_cells_extracted":"4376424","NMR_solvent_volume (uL)":"270","MS_solvent_volume (uL)":"963"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 7",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"none","Cells_per_mL":"17947","Number_of_cells_extracted":"4468803","NMR_solvent_volume (uL)":"276","MS_solvent_volume (uL)":"984"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 8",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 8","Cells_per_mL":"16462","Number_of_cells_extracted":"4099038","NMR_solvent_volume (uL)":"253","MS_solvent_volume (uL)":"902"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 9",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 9","Cells_per_mL":"16957","Number_of_cells_extracted":"4222293","NMR_solvent_volume (uL)":"261","MS_solvent_volume (uL)":"929"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 10",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 10","Cells_per_mL":"16462","Number_of_cells_extracted":"4099038","NMR_solvent_volume (uL)":"253","MS_solvent_volume (uL)":"902"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 11",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 11","Cells_per_mL":"15596","Number_of_cells_extracted":"3883404","NMR_solvent_volume (uL)":"240","MS_solvent_volume (uL)":"855"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 12",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 12","Cells_per_mL":"17081","Number_of_cells_extracted":"4253169","NMR_solvent_volume (uL)":"263","MS_solvent_volume (uL)":"936"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 13",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 13","Cells_per_mL":"16462","Number_of_cells_extracted":"4099038","NMR_solvent_volume (uL)":"253","MS_solvent_volume (uL)":"902"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 14",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"Atamarense 14","Cells_per_mL":"15101","Number_of_cells_extracted":"3760149","NMR_solvent_volume (uL)":"232","MS_solvent_volume (uL)":"828"}
},
{
"Subject ID":"-",
"Sample ID":"Atamarense 15",
"Factors":{"Treatment":"Alexandrium_tamarense"},
"Additional sample data":{"RAW_FILE_NAME":"none","Cells_per_mL":"17205","Number_of_cells_extracted":"4284045","NMR_solvent_volume (uL)":"265","MS_solvent_volume (uL)":"943"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Alexandrium cells were collected by vacuum filtration onto GF/F filters and quenched with liquid nitrogen. Frozen cells with filters were stored in foil (previously muffled for 3 h at 450 °C) at -80 °C until extraction.","COLLECTION_PROTOCOL_FILENAME":"Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome_protocol.pdf","SAMPLE_TYPE":"Algae","COLLECTION_METHOD":"Filtration and Freeze","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Metabolomes of toxic versus non-toxic species were compared using the following experimental pairings: A. tamarense (n=15) with A. catenella (n=15) (Experiment 1) and A. tamarense (n=15) with A. pacificum (n=15) (Experiment 2). The same non-toxic strain of A. tamarense was used in both experiments but the two experiments were conducted separately, in different months, to make the experiment manageable based on availability of batches grown from stock cultures. For both experiments, Alexandrium spp. cultures at a cell density of 12,000 to 13,000 cells mL-1 were split into fifteen 300 mL subcultures of each species which grew for two days. At the end of each experiment, during harvesting, a 1.0 mL aliquot from each culture was preserved with Lugol’s solution to measure cell concentrations","TREATMENT_PROTOCOL_FILENAME":"Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome_protocol.pdf","TREATMENT":"Species comparison"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Non polar extracts were dissolved with volumes calculated to account for different cell densities at the time of harvesting, to a concentration equivalent to 1.62 x 10^7 Alexandrium cells mL-1 in dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane (TMS) as internal standard for 1H nuclear magnetic resonance (NMR) spectroscopy analysis. The extracts were transferred to 3 mm NMR tubes. Extracts from Experiment 2 (A. tamarense-A. pacificum) were analyzed using a Bruker Avance IIIHD 700 MHz NMR spectrometer equipped with a 5 mm indirect broadband cryoprobe, because the 800 MHz instrument was unavailable at the time of data acquisition. Spectra of non-polar extracts from both experiments were acquired using a Bruker zg30 pulse sequence 1H NMR experiment compiled from 320 scans.","SAMPLEPREP_PROTOCOL_FILENAME":"Differentiating toxic and nontoxic congeneric harmful algae using the non-polar metabolome_protocol.pdf","EXTRACT_STORAGE":"-80℃"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR"},

"NM":{"INSTRUMENT_NAME":"Bruker Avance IIIHD","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","SPECTROMETER_FREQUENCY":"700 MHz","NMR_PROBE":"5 mm indirect broadband cryoprobe","NMR_SOLVENT":"Dimethyl sulfoxide d6 (99.9% atom d6-DMSO; Cambridge Isotope Labs) containing 0.1% trimethylsilane","NMR_TUBE_SIZE":"3 mm","PULSE_SEQUENCE":"zg30","NUMBER_OF_SCANS":"320","BASELINE_CORRECTION_METHOD":"Spline","BINNED_INCREMENT":"0.005 ppm","NMR_RESULTS_FILE":"Preprocessed_binned_Experiment2_ApvAt_NMRmetabolomics.txt UNITS:area under the curve"}

}