#METABOLOMICS WORKBENCH vanessa_mancini_20200829_105246 DATATRACK_ID:2154 STUDY_ID:ST001494 ANALYSIS_ID:AN002477 PROJECT_ID:PR001012
VERSION             	1
CREATED_ON             	September 29, 2020, 2:07 pm
#PROJECT
PR:PROJECT_TITLE                 	Embryo device MS study
PR:PROJECT_SUMMARY               	Metabolomics study of murine embryos cultured in an innovative microfluidic
PR:PROJECT_SUMMARY               	device to assess release of plastic-related compounds and embryo metabolic
PR:PROJECT_SUMMARY               	activity.
PR:INSTITUTE                     	University of Leeds
PR:DEPARTMENT                    	Electronic and Electrical Engineering
PR:LABORATORY                    	Bioelectronics Lab
PR:LAST_NAME                     	Mancini
PR:FIRST_NAME                    	Vanessa
PR:ADDRESS                       	Woodhouse Lane, Leeds, West Yorkshire, LS62HN, United Kingdom
PR:EMAIL                         	elvm@leeds.ac.uk
PR:PHONE                         	+447599197366
#STUDY
ST:STUDY_TITLE                   	Metabolomics of murine embryos cultured in a microfluidic device and comparison
ST:STUDY_TITLE                   	with traditional microdrops culture
ST:STUDY_SUMMARY                 	Global untargeted metabolomics study to analyse culture media extracted from an
ST:STUDY_SUMMARY                 	innovative microfluidic device or traditional microdrops in presence or absence
ST:STUDY_SUMMARY                 	of murine embryos to investigate PDMS-release of biomolecules and embryo
ST:STUDY_SUMMARY                 	metabolic activity.
ST:INSTITUTE                     	University of Leeds
ST:LAST_NAME                     	Mancini
ST:FIRST_NAME                    	Vanessa
ST:ADDRESS                       	Woodhouse Lane, Leeds, LS29JT
ST:EMAIL                         	elvm@leeds.ac.uk
ST:PHONE                         	+447599197366
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S1b	Device:Control_device	Group name=Day 0 KSOM
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S2b	Device:Control_device	Group name=Day 0 KSOM
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S3b	Device:Control_device	Group name=Day 0 KSOM
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S7	Device:No embryos_device	Group name=Day 5 KSOM_device
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S8	Device:No embryos_device	Group name=Day 5 KSOM_device
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S9	Device:No embryos_device	Group name=Day 5 KSOM_device
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S13	Device:Embryo culture media_device	Group name=Day 5 KSOM_device_embryos
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S14	Device:Embryo culture media_device	Group name=Day 5 KSOM_device_embryos
SUBJECT_SAMPLE_FACTORS           	-	SC_20190605_RPLCp_FMS_Embryo_S15	Device:Embryo culture media_device	Group name=Day 5 KSOM_device_embryos
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S01_T2	Device:Control_drops	Group name=Day 0 KSOM
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S02_T1	Device:Control_drops	Group name=Day 0 KSOM
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S03_T1	Device:Control_drops	Group name=Day 0 KSOM
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S07_T1	Device:No embryos_drops	Group name=Day 4 KSOM_drop
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S08_T1	Device:No embryos_drops	Group name=Day 4 KSOM_drop
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S09_T2	Device:No embryos_drops	Group name=Day 4 KSOM_drop
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S13_T1	Device:Embryo culture media_drops	Group name=Day 4 KSOM_drop_embryos
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S14_T2	Device:Embryo culture media_drops	Group name=Day 4 KSOM_drop_embryos
SUBJECT_SAMPLE_FACTORS           	-	SC_20191202_FMS_Embryo_S15_T1	Device:Embryo culture media_drops	Group name=Day 4 KSOM_drop_embryos
#COLLECTION
CO:COLLECTION_SUMMARY            	Samples were collected from microdrops and microfluidic devices when embryos
CO:COLLECTION_SUMMARY            	developed to fully expanded blastocyst stage, to allow stage-matched comparison
CO:COLLECTION_SUMMARY            	of embryo metabolite production/consumption.
CO:SAMPLE_TYPE                   	Blastocysts
#TREATMENT
TR:TREATMENT_SUMMARY             	Control KSOM: fresh medium at day 0 not incubated in devices or microdrops. Day
TR:TREATMENT_SUMMARY             	4 KSOM_drop: medium incubated in microdrops for 4 days without embryos Day 5
TR:TREATMENT_SUMMARY             	KSOM_device: medium incubated in devices for 5 days without embryos Day 4
TR:TREATMENT_SUMMARY             	KSOM_drop_embryos: medium incubated in microdrops for 4 days with embryos Day 5
TR:TREATMENT_SUMMARY             	KSOM_device_embryos: medium incubated in devices for 5 days with embryos
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Culture media samples (100 µl) were thawed on ice and prepared using previously
SP:SAMPLEPREP_SUMMARY            	described methods. Briefly, 300 µL of dry ice cooled methanol was added to
SP:SAMPLEPREP_SUMMARY            	individual culture medium samples and incubated overnight at -80°C; individual
SP:SAMPLEPREP_SUMMARY            	samples were spun down to remove proteins and subsequent supernatant used for
SP:SAMPLEPREP_SUMMARY            	analyses. Samples were separated and analysed using reverse-phase liquid
SP:SAMPLEPREP_SUMMARY            	chromatography connected to a a Thermo Scientific Q Exactive HF (LC-Hybrid
SP:SAMPLEPREP_SUMMARY            	Quadrupole-Orbitrap MS/MS) instrument using positive ion mode MS.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Thermo Hypersil Gold (1.9 µm, 2.1mm x 100 mm)
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive HF hybrid Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Full MS analyses were acquired over a mass range of m/z 70-1050 under an ESI
MS:MS_COMMENTS                   	positive profile mode. Full mass scan was used at a resolution of 120,000 with a
MS:MS_COMMENTS                   	scan rate at ∼3.5 Hz Raw data were imported, processed, normalized, and
MS:MS_COMMENTS                   	reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK). All FMS
MS:MS_COMMENTS                   	sample runs were aligned against a FMS QC pool reference, with alignment to the
MS:MS_COMMENTS                   	reference being ≥ 96%, demonstrating the reproducibility of the RPLC column
MS:MS_COMMENTS                   	separation method. Peak picking, with a minimum threshold of 100,000 ion
MS:MS_COMMENTS                   	intensity, was performed for individual aligned runs based on an aggregate run
MS:MS_COMMENTS                   	(representative of all ion peaks detected in all samples).
MS:MS_RESULTS_FILE               	ST001494_AN002477_Results.txt	UNITS:peak area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END