{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001494","ANALYSIS_ID":"AN002476","VERSION":"1","CREATED_ON":"September 29, 2020, 2:07 pm"},

"PROJECT":{"PROJECT_TITLE":"Embryo device MS study","PROJECT_SUMMARY":"Metabolomics study of murine embryos cultured in an innovative microfluidic device to assess release of plastic-related compounds and embryo metabolic activity.","INSTITUTE":"University of Leeds","DEPARTMENT":"Electronic and Electrical Engineering","LABORATORY":"Bioelectronics Lab","LAST_NAME":"Mancini","FIRST_NAME":"Vanessa","ADDRESS":"Woodhouse Lane, Leeds, West Yorkshire, LS62HN, United Kingdom","EMAIL":"elvm@leeds.ac.uk","PHONE":"+447599197366"},

"STUDY":{"STUDY_TITLE":"Metabolomics of murine embryos cultured in a microfluidic device and comparison with traditional microdrops culture","STUDY_SUMMARY":"Global untargeted metabolomics study to analyse culture media extracted from an innovative microfluidic device or traditional microdrops in presence or absence of murine embryos to investigate PDMS-release of biomolecules and embryo metabolic activity.","INSTITUTE":"University of Leeds","LAST_NAME":"Mancini","FIRST_NAME":"Vanessa","ADDRESS":"Woodhouse Lane, Leeds, LS29JT","EMAIL":"elvm@leeds.ac.uk","PHONE":"+447599197366"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S1b",
"Factors":{"Device":"Control_device"},
"Additional sample data":{"Group name":"Day 0 KSOM"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S2b",
"Factors":{"Device":"Control_device"},
"Additional sample data":{"Group name":"Day 0 KSOM"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S3b",
"Factors":{"Device":"Control_device"},
"Additional sample data":{"Group name":"Day 0 KSOM"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S7",
"Factors":{"Device":"No embryos_device"},
"Additional sample data":{"Group name":"Day 5 KSOM_device"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S8",
"Factors":{"Device":"No embryos_device"},
"Additional sample data":{"Group name":"Day 5 KSOM_device"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S9",
"Factors":{"Device":"No embryos_device"},
"Additional sample data":{"Group name":"Day 5 KSOM_device"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S13",
"Factors":{"Device":"Embryo culture media_device"},
"Additional sample data":{"Group name":"Day 5 KSOM_device_embryos"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S14",
"Factors":{"Device":"Embryo culture media_device"},
"Additional sample data":{"Group name":"Day 5 KSOM_device_embryos"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20190605_RPLCp_FMS_Embryo_S15",
"Factors":{"Device":"Embryo culture media_device"},
"Additional sample data":{"Group name":"Day 5 KSOM_device_embryos"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S01_T2",
"Factors":{"Device":"Control_drops"},
"Additional sample data":{"Group name":"Day 0 KSOM"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S02_T1",
"Factors":{"Device":"Control_drops"},
"Additional sample data":{"Group name":"Day 0 KSOM"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S03_T1",
"Factors":{"Device":"Control_drops"},
"Additional sample data":{"Group name":"Day 0 KSOM"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S07_T1",
"Factors":{"Device":"No embryos_drops"},
"Additional sample data":{"Group name":"Day 4 KSOM_drop"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S08_T1",
"Factors":{"Device":"No embryos_drops"},
"Additional sample data":{"Group name":"Day 4 KSOM_drop"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S09_T2",
"Factors":{"Device":"No embryos_drops"},
"Additional sample data":{"Group name":"Day 4 KSOM_drop"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S13_T1",
"Factors":{"Device":"Embryo culture media_drops"},
"Additional sample data":{"Group name":"Day 4 KSOM_drop_embryos"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S14_T2",
"Factors":{"Device":"Embryo culture media_drops"},
"Additional sample data":{"Group name":"Day 4 KSOM_drop_embryos"}
},
{
"Subject ID":"-",
"Sample ID":"SC_20191202_FMS_Embryo_S15_T1",
"Factors":{"Device":"Embryo culture media_drops"},
"Additional sample data":{"Group name":"Day 4 KSOM_drop_embryos"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Samples were collected from microdrops and microfluidic devices when embryos developed to fully expanded blastocyst stage, to allow stage-matched comparison of embryo metabolite production/consumption.","SAMPLE_TYPE":"Blastocysts"},

"TREATMENT":{"TREATMENT_SUMMARY":"Control KSOM: fresh medium at day 0 not incubated in devices or microdrops. Day 4 KSOM_drop: medium incubated in microdrops for 4 days without embryos Day 5 KSOM_device: medium incubated in devices for 5 days without embryos Day 4 KSOM_drop_embryos: medium incubated in microdrops for 4 days with embryos Day 5 KSOM_device_embryos: medium incubated in devices for 5 days with embryos"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Culture media samples (100 µl) were thawed on ice and prepared using previously described methods. Briefly, 300 µL of dry ice cooled methanol was added to individual culture medium samples and incubated overnight at -80°C; individual samples were spun down to remove proteins and subsequent supernatant used for analyses. Samples were separated and analysed using reverse-phase liquid chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Hypersil Gold (1.9 µm, 2.1mm x 100 mm)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI positive profile mode. Full mass scan was used at a resolution of 120,000 with a scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS sample runs were aligned against a FMS QC pool reference, with alignment to the reference being ≥ 96%, demonstrating the reproducibility of the RPLC column separation method. Peak picking, with a minimum threshold of 100,000 ion intensity, was performed for individual aligned runs based on an aggregate run (representative of all ion peaks detected in all samples).","MS_RESULTS_FILE":"ST001494_AN002476_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}