#METABOLOMICS WORKBENCH krystinemansfield_20250218_142800 DATATRACK_ID:5645 STUDY_ID:ST003775 ANALYSIS_ID:AN006201 PROJECT_ID:PR002353
VERSION             	1
CREATED_ON             	February 20, 2025, 7:53 am
#PROJECT
PR:PROJECT_TITLE                 	miR-126 driven metabolomics in inv(16) AML mouse model
PR:PROJECT_SUMMARY               	LSCs have been shown to more highly express miR-126 in AML, and that inhibition
PR:PROJECT_SUMMARY               	reduces LSCs and prolongs subject survivial. To further study the mechnanism of
PR:PROJECT_SUMMARY               	this, we performed untargeted metabolomics to identify differentially abundant
PR:PROJECT_SUMMARY               	metabolites in inv(16) AML model mice.
PR:INSTITUTE                     	Translational Genomics Research Institute
PR:LAST_NAME                     	Pirrotte
PR:FIRST_NAME                    	Patrick
PR:ADDRESS                       	445 N 5th St, Phoenix, AZ, 85004, USA
PR:EMAIL                         	ppirrotte@tgen.org
PR:PHONE                         	602-343-8454
#STUDY
ST:STUDY_TITLE                   	miR-126 metabolomics in inv(16) mice
ST:STUDY_SUMMARY                 	Untargeted metabolomics using LC-MS/MS was used to identify and classify
ST:STUDY_SUMMARY                 	differentially abundant metabolites in inv(16) AML model mice (n=3) compared to
ST:STUDY_SUMMARY                 	controls (n=3).
ST:INSTITUTE                     	Translational Genomics Research Institute
ST:LAST_NAME                     	Pirrotte
ST:FIRST_NAME                    	Patrick
ST:ADDRESS                       	445 N 5th St, Phoenix, AZ, 85004, USA
ST:EMAIL                         	ppirrotte@tgen.org
ST:PHONE                         	614-302-8454
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Mus musculus
SU:TAXONOMY_ID                   	10090
SU:GENDER                        	Male and female
#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           	T01xCONxHWx4496	T01xCONxHWx4496RPpos	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02A_R_T01xCONxHWx4496RPpos_17NOV21_PLA_HUM_LUM_0000_04AB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T02xCONxCx4498	T02xCONxCx4498RPpos	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02A_R_T02xCONxCx4498RPpos_17NOV21_PLA_HUM_LUM_0000_04AB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T03xCONxCx4507	T03xCONxCx4507RPpos	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02A_R_T03xCONxCx4507RPpos_17NOV21_PLA_HUM_LUM_0000_04AB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T04xINV16xCHWx4521	T04xINV16xCHWx4521RPpos	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02A_R_T04xINV16xCHWx4521RPpos_17NOV21_PLA_HUM_LUM_0000_04AB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T05xINV16xCHWx4522	T05xINV16xCHWx4522RPpos	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02A_R_T05xINV16xCHWx4522RPpos_17NOV21_PLA_HUM_LUM_0000_04AB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T06xINV16xCHWx4502	T06xINV16xCHWx4502RPpos	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02A_R_T06xINV16xCHWx4502RPpos_17NOV21_PLA_HUM_LUM_0000_04AB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T01xCONxHWx4496	T01xCONxHWx4496RPneg	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02B_R_T01xCONxHWx4496RPneg_17NOV21_PLA_HUM_LUM_0000_04BB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T02xCONxCx4498	T02xCONxCx4498RPneg	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02B_R_T02xCONxCx4498RPneg_17NOV21_PLA_HUM_LUM_0000_04BB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T03xCONxCx4507	T03xCONxCx4507RPneg	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02B_R_T03xCONxCx4507RPneg_17NOV21_PLA_HUM_LUM_0000_04BB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T04xINV16xCHWx4521	T04xINV16xCHWx4521RPneg	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02B_R_T04xINV16xCHWx4521RPneg_17NOV21_PLA_HUM_LUM_0000_04BB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T05xINV16xCHWx4522	T05xINV16xCHWx4522RPneg	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02B_R_T05xINV16xCHWx4522RPneg_17NOV21_PLA_HUM_LUM_0000_04BB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T06xINV16xCHWx4502	T06xINV16xCHWx4502RPneg	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02B_R_T06xINV16xCHWx4502RPneg_17NOV21_PLA_HUM_LUM_0000_04BB_15MIN_KP_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T01xCONxHWx4496	T01xCONxHWx4496HILICpos	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02C_R_T01xCONxHWx4496HILICpos_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T02xCONxCx4498	T02xCONxCx4498HILICpos	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02C_R_T02xCONxCx4498HILICpos_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T03xCONxCx4507	T03xCONxCx4507HILICpos	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02C_R_T03xCONxCx4507HILICpos_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T04xINV16xCHWx4521	T04xINV16xCHWx4521HILICpos	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02C_R_T04xINV16xCHWx4521HILICpos_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T05xINV16xCHWx4522	T05xINV16xCHWx4522HILICpos	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02C_R_T05xINV16xCHWx4522HILICpos_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T06xINV16xCHWx4502	T06xINV16xCHWx4502HILICpos	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02C_R_T06xINV16xCHWx4502HILICpos_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T01xCONxHWx4496	T01xCONxHWx4496HILICneg	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02D_R_T01xCONxHWx4496HILICneg_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T02xCONxCx4498	T02xCONxCx4498HILICneg	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02D_R_T02xCONxCx4498HILICneg_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T03xCONxCx4507	T03xCONxCx4507HILICneg	Sample source:Mouse cells | Genotype:Control	RAW_FILE_NAME(Raw file name)=088_0004_02D_R_T03xCONxCx4507HILICneg_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T04xINV16xCHWx4521	T04xINV16xCHWx4521HILICneg	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02D_R_T04xINV16xCHWx4521HILICneg_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T05xINV16xCHWx4522	T05xINV16xCHWx4522HILICneg	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02D_R_T05xINV16xCHWx4522HILICneg_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
SUBJECT_SAMPLE_FACTORS           	T06xINV16xCHWx4502	T06xINV16xCHWx4502HILICneg	Sample source:Mouse cells | Genotype:inv(16)	RAW_FILE_NAME(Raw file name)=088_0004_02D_R_T06xINV16xCHWx4502HILICneg_19NOV21_PLA_HUM_LUM_0000_04AB_15MIN_ART_KP_01.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	BM mononuclear cells were collected from femurs, tibias, and pelvis using a
CO:COLLECTION_SUMMARY            	mortar and pestle.
CO:SAMPLE_TYPE                   	Bone marrow
#TREATMENT
TR:TREATMENT_SUMMARY             	CM expression was induced by polyinosinic–polycytidylic acid [poly (I:C)]
TR:TREATMENT_SUMMARY             	intraperitoneally, treatment with 14 mg/kg/dose every other day for a total of 7
TR:TREATMENT_SUMMARY             	doses. Age-matched and poly induced Cbfb56M/+ or Mx1-Cre littermates were used
TR:TREATMENT_SUMMARY             	as controls.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Lineage-negative (Lin-) cells were enriched using EasySep™ negative selection
SP:SAMPLEPREP_SUMMARY            	reagents. These cells were then stained with fluorescently labeled antibodies in
SP:SAMPLEPREP_SUMMARY            	PBS with 0.5% BSA for 15 min at 4°C. After washing, cells were resuspended in
SP:SAMPLEPREP_SUMMARY            	PBS with 2% BSA and sorted. After sorting, cells were washed once with PBS and
SP:SAMPLEPREP_SUMMARY            	cell pellets were stored in -80. Cells were resuspended in methanol and vortexed
SP:SAMPLEPREP_SUMMARY            	for 30s, then subjected to 3 30 second freeze-thaw cycles to lyse them. Lysates
SP:SAMPLEPREP_SUMMARY            	were centrifuged and supernatants were split into two aliquots, one for HILIC
SP:SAMPLEPREP_SUMMARY            	and one for reverse phase acquisition.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Orbitrap Fusion Lumos
CH:COLUMN_NAME                   	Hypersil GOLD C18 (175 Å, 1.9 µm, 2.1 × 150 mm)
CH:SOLVENT_A                     	water, 0.1% formic acid, v/v
CH:SOLVENT_B                     	acetonitrile, 0.1% formic acid, v/v
CH:FLOW_GRADIENT                 	linear
CH:FLOW_RATE                     	0.35 mL/min
CH:COLUMN_TEMPERATURE            	45
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Orbitrap Fusion Lumos Tribrid
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Samples were randomized individually for each chromatography. MS1 data were
MS:MS_COMMENTS                   	acquired over a mass range of 70–1500 m/z in the orbitrap 60,000 resolution.
MS:MS_COMMENTS                   	MS2 data were acquired in AcquireX mode with the iterative precursor exclusion
MS:MS_COMMENTS                   	workflow, and a stepped HCD collision energy at 20, 35 and 50, at 30,000
MS:MS_COMMENTS                   	resolution in the orbitrap.
MS:MS_RESULTS_FILE               	ST003775_AN006201_Results.txt	UNITS:area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END