#METABOLOMICS WORKBENCH jgengatharan_20240729_090646 DATATRACK_ID:5044 STUDY_ID:ST003369 ANALYSIS_ID:AN005574 PROJECT_ID:PR002085
VERSION             	1
CREATED_ON             	July 29, 2024, 9:17 am
#PROJECT
PR:PROJECT_TITLE                 	Altered sphingolipid biosynthetic flux and lipoprotein trafficking contribute to
PR:PROJECT_TITLE                 	trans fat-induced atherosclerosis
PR:PROJECT_SUMMARY               	The goal of the project is to determine the role of sphingolipid metabolism in
PR:PROJECT_SUMMARY               	atherosclerosis induced by dietary trans fat. We analyzed lipid metabolites in
PR:PROJECT_SUMMARY               	Huh7 cells following various fatty acid treatments, with specific focus on cis
PR:PROJECT_SUMMARY               	and trans unsaturated fatty acids. Additionally, we analyzed lipid metabolites
PR:PROJECT_SUMMARY               	in plasma and liver of Ldlr-/- mice fed high-fat diets enriched in cis or trans
PR:PROJECT_SUMMARY               	fatty acids in the presence or absence of myriocin, a pharmacological inhibitor
PR:PROJECT_SUMMARY               	of SPT, the initial rate-limiting enzyme of sphingolipid biosynthesis.
PR:INSTITUTE                     	Salk Institute for Biological Studies
PR:LAST_NAME                     	Gengatharan
PR:FIRST_NAME                    	Jivani
PR:ADDRESS                       	10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
PR:EMAIL                         	jivani14@gmail.com
PR:PHONE                         	(858) 453-4100
#STUDY
ST:STUDY_TITLE                   	Incorporation of oleate-d9 and elaidate-d17 in sphingolipids in Huh7 cells.
ST:STUDY_SUMMARY                 	We analyzed sphingolipids in Huh7 cells treated with BSA-oleate-d9 or
ST:STUDY_SUMMARY                 	BSA-elaidate-d17.
ST:INSTITUTE                     	Salk Institute for Biological Studies
ST:LAST_NAME                     	Gengatharan
ST:FIRST_NAME                    	Jivani
ST:ADDRESS                       	10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
ST:EMAIL                         	jivani14@gmail.com
ST:PHONE                         	(858) 453-4100
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:CELL_STRAIN_DETAILS           	Huh7
#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           	-	Huh7cells_C8SL2_d9oleic1	Sample source:Huh7 cells | Treatment:BSA-oleate-d9	RAW_FILE_NAME(Raw file name)=Huh7cells_C8SL2_d9oleic1.d
SUBJECT_SAMPLE_FACTORS           	-	Huh7cells_C8SL2_d9oleic2	Sample source:Huh7 cells | Treatment:BSA-oleate-d9	RAW_FILE_NAME(Raw file name)=Huh7cells_C8SL2_d9oleic2.d
SUBJECT_SAMPLE_FACTORS           	-	Huh7cells_C8SL2_d9oleic3	Sample source:Huh7 cells | Treatment:BSA-oleate-d9	RAW_FILE_NAME(Raw file name)=Huh7cells_C8SL2_d9oleic3.d
SUBJECT_SAMPLE_FACTORS           	-	Huh7cells_C8SL2_d17elaidic1	Sample source:Huh7 cells | Treatment:BSA-elaidate-d17	RAW_FILE_NAME(Raw file name)=Huh7cells_C8SL2_d17elaidic1.d
SUBJECT_SAMPLE_FACTORS           	-	Huh7cells_C8SL2_d17elaidic2	Sample source:Huh7 cells | Treatment:BSA-elaidate-d17	RAW_FILE_NAME(Raw file name)=Huh7cells_C8SL2_d17elaidic2.d
SUBJECT_SAMPLE_FACTORS           	-	Huh7cells_C8SL2_d17elaidic3	Sample source:Huh7 cells | Treatment:BSA-elaidate-d17	RAW_FILE_NAME(Raw file name)=Huh7cells_C8SL2_d17elaidic3.d
#COLLECTION
CO:COLLECTION_SUMMARY            	Cells (~400,000 cells) were spiked with the following internal standards: 20
CO:COLLECTION_SUMMARY            	pmol sphinganine-d7 (Avanti Polar Lipids, Cat# 860658), deoxysphinganine-d3
CO:COLLECTION_SUMMARY            	(Avanti Polar Lipids, Cat# 860474), 100 pmol d18:0-d7/13:0 dihydroceramide
CO:COLLECTION_SUMMARY            	(Avanti Polar Lipids, Cat# 330726), 200 pmol d18:1-d7/15:0 ceramide (Avanti
CO:COLLECTION_SUMMARY            	Polar Lipids, Cat# 860681), 100 pmol d18:1-d7/15:0 glucosylceramide (Avanti
CO:COLLECTION_SUMMARY            	Polar Lipids, Cat# 330729), 100 pmol d18:1-d7/15:0 lactosylceramide (Avanti
CO:COLLECTION_SUMMARY            	Polar Lipids, Cat# 330727), 200 pmol sphingosine-d7 (Avanti Polar Lipids, Cat#
CO:COLLECTION_SUMMARY            	860657). Cells were scraped with 0.5 mL methanol and 0.5 mL H2O.
CO:SAMPLE_TYPE                   	Cultured cells
#TREATMENT
TR:TREATMENT_SUMMARY             	Huh7 cells were treated with 1) 100 µM BSA-oleate-d9 or 2) 100 µM
TR:TREATMENT_SUMMARY             	BSA-elaidate-d17 for 48 hours in delipidated media.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Cells (~400,000 cells) were spiked with the following internal standards: 20
SP:SAMPLEPREP_SUMMARY            	pmol sphinganine-d7 (Avanti Polar Lipids, Cat# 860658), deoxysphinganine-d3
SP:SAMPLEPREP_SUMMARY            	(Avanti Polar Lipids, Cat# 860474), 100 pmol d18:0-d7/13:0 dihydroceramide
SP:SAMPLEPREP_SUMMARY            	(Avanti Polar Lipids, Cat# 330726), 200 pmol d18:1-d7/15:0 ceramide (Avanti
SP:SAMPLEPREP_SUMMARY            	Polar Lipids, Cat# 860681), 100 pmol d18:1-d7/15:0 glucosylceramide (Avanti
SP:SAMPLEPREP_SUMMARY            	Polar Lipids, Cat# 330729), 100 pmol d18:1-d7/15:0 lactosylceramide (Avanti
SP:SAMPLEPREP_SUMMARY            	Polar Lipids, Cat# 330727), 200 pmol sphingosine-d7 (Avanti Polar Lipids, Cat#
SP:SAMPLEPREP_SUMMARY            	860657). Cells were scraped with 0.5 mL methanol and 0.5 mL H2O. Homogenate
SP:SAMPLEPREP_SUMMARY            	aliquot of 100 µL was taken to determine protein content using the BCA protein
SP:SAMPLEPREP_SUMMARY            	assay (Thermo Fisher Scientific). The remaining homogenate was transferred to a
SP:SAMPLEPREP_SUMMARY            	new Eppendorf tube and 1 mL chloroform was added. For plasma or media, 0.5 mL
SP:SAMPLEPREP_SUMMARY            	methanol, 0.5 mL H2O, and 1 mL chloroform were added directly. Samples were
SP:SAMPLEPREP_SUMMARY            	vortexed for 5 min and centrifuged for 5 min at 4 ˚C at 15,000g. The organic
SP:SAMPLEPREP_SUMMARY            	phase was collected and 2 μL of formic acid was added to the remaining polar
SP:SAMPLEPREP_SUMMARY            	phase which was re-extracted with 1 mL of chloroform. Combined organic phases
SP:SAMPLEPREP_SUMMARY            	were dried under nitrogen. After dried extracts for cells were resuspended in 60
SP:SAMPLEPREP_SUMMARY            	µl Buffer B, 5 µL of sample was injected.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Agilent 1260 Infinity II
CH:COLUMN_NAME                   	Peeke Scientific Spectra C8SR (150 x 3.0 mm, 3μm)
CH:SOLVENT_A                     	100% water; 0.2% formic acid; 2 mM ammonium formate
CH:SOLVENT_B                     	100% methanol; 0.2% formic acid; 1 mM ammonium formate
CH:FLOW_GRADIENT                 	0 min, 82% B; 3 min, 82% B; 4 min, 90% B; 18 min, 99% B; 25 min, 99% B; 27 min,
CH:FLOW_GRADIENT                 	82% B; 30 min, 82% B
CH:FLOW_RATE                     	0.5 ml/min
CH:COLUMN_TEMPERATURE            	40
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6460 QQQ
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Agilent Masshunter
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Peak area
MS_METABOLITE_DATA_START
Samples	Huh7cells_C8SL2_d9oleic1	Huh7cells_C8SL2_d9oleic2	Huh7cells_C8SL2_d9oleic3	Huh7cells_C8SL2_d17elaidic1	Huh7cells_C8SL2_d17elaidic2	Huh7cells_C8SL2_d17elaidic3
Factors	Sample source:Huh7 cells | Treatment:BSA-oleate-d9	Sample source:Huh7 cells | Treatment:BSA-oleate-d9	Sample source:Huh7 cells | Treatment:BSA-oleate-d9	Sample source:Huh7 cells | Treatment:BSA-elaidate-d17	Sample source:Huh7 cells | Treatment:BSA-elaidate-d17	Sample source:Huh7 cells | Treatment:BSA-elaidate-d17
Lac-Cer d18:1-d7/15:0	13801	14258	15786	12552	18506	16908
Lac-Cer d20:2-d17/24:0				1640	1460	1016
Lac-Cer d20:2-d17/24:1-d17				865	1285	1050
SM d34:2-d34				336249	374139	318226
SM d36:2-d17				1766032	1869610	1724339
SM d36:2-d9	346181	323223	337772			
SM d36:3-d17				195348	228413	189190
SM d36:3-d34				4461235	4929934	4503866
SM d38:2-d17				416198	465160	370086
SM d38:2-d9	250245	185249	216222			
SM d38:3-d34				1717849	1341775	1790553
SM d40:2-d17				1254613	1442670	1213517
SM d40:2-d9	989574	900301	1011671			
SM d40:3-d34				1171515	1254900	1100048
SM d42:2-d17				1682811	1964989	1689875
SM d42:2-d34				178456	191907	174251
SM d42:2-d9	10313030	10050197	11405818			
SM d42:3-d17				517272	519762	490770
SM d42:3-d34				3444213	3661266	3314513
SM d42:3-d9	403057	283190	500805			
SM d44:2-d9	458785	321691	674103			
SM d44:3-d17				312567	283395	253109
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Precursor Ion	Product Ion
Lac-Cer d18:1-d7/15:0	855.7	271.2
Lac-Cer d20:2-d17/24:0	1017.7	307.4
Lac-Cer d20:2-d17/24:1-d17	1032.7	307.4
SM d34:2-d34	735.6	184
SM d36:2-d17	746.6	184
SM d36:2-d9	738.6	184
SM d36:3-d17	744.6	184
SM d36:3-d34	761.6	184
SM d38:2-d17	774.6	184
SM d38:2-d9	766.6	184
SM d38:3-d34	789.6	184
SM d40:2-d17	802.7	184
SM d40:2-d9	794.7	184
SM d40:3-d34	817.6	184
SM d42:2-d17	830.7	184
SM d42:2-d34	847.7	184
SM d42:2-d9	822.7	184
SM d42:3-d17	828.7	184
SM d42:3-d34	845.7	184
SM d42:3-d9	820.7	184
SM d44:2-d9	850.7	184
SM d44:3-d17	856.7	184
METABOLITES_END
#END