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MB Sample ID: SA193930

Local Sample ID:	4T1-19_R15-
Subject ID:	SU002140
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

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Subject:

Subject ID:	SU002140
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
4T1-19_R15-	SA193930	FL023746	Upper_Arm_SkM	Tissue
4T1-19_R15-	SA193930	FL023746	Tumor	Treatment

Collection:

Collection ID:	CO002133
Collection Summary:	Lung and skeletal muscle (TA and bulk muscles from the upper arm) were collected upon necropsy and imaged for mCherry+ 4T1-SkM lesions (Zeiss AxioZoom). Once a mCherry+ lesion was identified, the region was excised, leaving as little tissue margins as possible. The sample was weighed and then flash frozen using LN2. Healthy lung and skeletal muscle samples were collected through the same process, without the mCherry imaging step. 4T1-parental and 4T1-SkM cells were plated in 6-well plates at an initial density of 50,000 cells/well and collected 48h later (final density ~275,000 cells/well). Wells were washed twice with 1x PBS and cells were scraped into 1.5 mL microcentrifuge tubes and spun at 16,000 x g for 3 minutes. Samples were then flash frozen and stored at -80°C until ready to process.
Sample Type:	Lung

Treatment:

Treatment ID:	TR002152
Treatment Summary:	Lung and skeletal muscle (TA and bulk muscles from the upper arm) were collected upon necropsy and imaged for mCherry+ 4T1-SkM lesions (Zeiss AxioZoom). Once a mCherry+ lesion was identified, the region was excised, leaving as little tissue margins as possible. The sample was weighed and then flash frozen using LN2. Healthy lung and skeletal muscle samples were collected through the same process, without the mCherry imaging step. 4T1-parental and 4T1-SkM cells were plated in 6-well plates at an initial density of 50,000 cells/well and collected 48h later (final density ~275,000 cells/well). Wells were washed twice with 1x PBS and cells were scraped into 1.5 mL microcentrifuge tubes and spun at 16,000 x g for 3 minutes. Samples were then flash frozen and stored at -80°C until ready to process.

Treatment ID:

TR002152

Treatment Summary:

Lung and skeletal muscle (TA and bulk muscles from the upper arm) were collected upon necropsy and imaged for mCherry+ 4T1-SkM lesions (Zeiss AxioZoom). Once a mCherry+ lesion was identified, the region was excised, leaving as little tissue margins as possible. The sample was weighed and then flash frozen using LN2. Healthy lung and skeletal muscle samples were collected through the same process, without the mCherry imaging step. 4T1-parental and 4T1-SkM cells were plated in 6-well plates at an initial density of 50,000 cells/well and collected 48h later (final density ~275,000 cells/well). Wells were washed twice with 1x PBS and cells were scraped into 1.5 mL microcentrifuge tubes and spun at 16,000 x g for 3 minutes. Samples were then flash frozen and stored at -80°C until ready to process.

Sample Preparation:

Sampleprep ID:	SP002146
Sampleprep Summary:	Prior to LC-MS analysis, tissue samples were weighed and resuspended in pre-chilled (-20°C) methanol:acetonitrile:water (5:3:2, v:v) to a final concentration of 30 mg/ml, cell samples were placed on ice and re-suspended with methanol:acetonitrile:water (5:3:2, v:v) at a concentration of 2x106 cells/mL, and media samples were extracted with the same solution at a dilution of 1:25 (v/v). Suspensions were vortexed continuously for 30 min at 4°C. Insoluble material was removed by centrifugation at 18,000 g for 10 min at 4°C and supernatants were isolated for metabolomics analysis by UHPLC-MS. Analyses were performed as previously published85,86. Injection volumes for tissue, cell, and media extracts were 2 L, 10 L, and 10L, respectively. The analytical platform employs a Vanquish UHPLC system (ThermoFisher) coupled online to a Q Exactive mass spectrometer (ThermoFisher). Samples were resolved over a Kinetex C18 column, 2.1 x 150 mm, 1.7 m particle size (Phenomenex, Torrance, CA) equipped with a guard column (SecurityGuardTM Ultracartridge – UHPLC C18 for 2.1 mm ID Columns – AJO-8782 – Phenomenex, Torrance, CA) using an aqueous phase (A) of water and 0.1% formic acid and a mobile phase (B) of acetonitrile and 0.1% formic acid for positive ion polarity mode, and an aqueous phase (A) of water:acetonitrile (95:5) with 1 mM ammonium acetate, and a mobile phase (B) of acetonitrile:water (95:5) with 1 mM ammonium acetate for negative ion polarity mode. Samples were eluted from the column using either an isocratic elution of 5% B flowed at 250 L/min and 25°C or a gradient from 5% to 95% B over 1 min, followed by an isocratic hold at 95% B for 2 min, flowed at 400 L/min and 45°C. The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)92.

Sampleprep ID:

SP002146

Sampleprep Summary:

Prior to LC-MS analysis, tissue samples were weighed and resuspended in pre-chilled (-20°C) methanol:acetonitrile:water (5:3:2, v:v) to a final concentration of 30 mg/ml, cell samples were placed on ice and re-suspended with methanol:acetonitrile:water (5:3:2, v:v) at a concentration of 2x106 cells/mL, and media samples were extracted with the same solution at a dilution of 1:25 (v/v). Suspensions were vortexed continuously for 30 min at 4°C. Insoluble material was removed by centrifugation at 18,000 g for 10 min at 4°C and supernatants were isolated for metabolomics analysis by UHPLC-MS. Analyses were performed as previously published85,86. Injection volumes for tissue, cell, and media extracts were 2 L, 10 L, and 10L, respectively. The analytical platform employs a Vanquish UHPLC system (ThermoFisher) coupled online to a Q Exactive mass spectrometer (ThermoFisher). Samples were resolved over a Kinetex C18 column, 2.1 x 150 mm, 1.7 m particle size (Phenomenex, Torrance, CA) equipped with a guard column (SecurityGuardTM Ultracartridge – UHPLC C18 for 2.1 mm ID Columns – AJO-8782 – Phenomenex, Torrance, CA) using an aqueous phase (A) of water and 0.1% formic acid and a mobile phase (B) of acetonitrile and 0.1% formic acid for positive ion polarity mode, and an aqueous phase (A) of water:acetonitrile (95:5) with 1 mM ammonium acetate, and a mobile phase (B) of acetonitrile:water (95:5) with 1 mM ammonium acetate for negative ion polarity mode. Samples were eluted from the column using either an isocratic elution of 5% B flowed at 250 L/min and 25°C or a gradient from 5% to 95% B over 1 min, followed by an isocratic hold at 95% B for 2 min, flowed at 400 L/min and 45°C. The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)92.

Combined analysis:

Analysis ID	AN003350	AN003351
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	QExactive	QExactive
Column	Kinetix C18 (100 x 2.1mm)	Kinetix C18 (100 x 2.1mm)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	AU	AU

Chromatography:

Chromatography ID:	CH002481
Instrument Name:	QExactive
Column Name:	Kinetix C18 (100 x 2.1mm)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003119
Analysis ID:	AN003350
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)
Ion Mode:	POSITIVE

MS ID:	MS003120
Analysis ID:	AN003351
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)
Ion Mode:	NEGATIVE