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MB Sample ID: SA185837

Local Sample ID:	RH2-09
Subject ID:	SU002067
Subject Type:	Cultured cells
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	Fbxo7LacZ mice (Fbxo7tm1a(EUCOMM)Hmgu on a C57BL/6J background) were bred as heterozygous crosses
Age Or Age Range:	WT, heterozygous and homozygous littermates were harvested between 6-9 weeks.
Gender:	Male and female
Subject Comments:	All experiments in mice were performed in accordance with the UK Animals (Scientific Procedures) Act 1986 and ARRIVE guidelines. Animal licences were approved by the Home Office and the University of Cambridge's Animal Welfare & Ethical Review Body Standing Committee. Experiments were performed under Home Office licence PPL 70/9001.

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Subject:

Subject ID:	SU002067
Subject Type:	Cultured cells
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	Fbxo7LacZ mice (Fbxo7tm1a(EUCOMM)Hmgu on a C57BL/6J background) were bred as heterozygous crosses
Age Or Age Range:	WT, heterozygous and homozygous littermates were harvested between 6-9 weeks.
Gender:	Male and female
Subject Comments:	All experiments in mice were performed in accordance with the UK Animals (Scientific Procedures) Act 1986 and ARRIVE guidelines. Animal licences were approved by the Home Office and the University of Cambridge's Animal Welfare & Ethical Review Body Standing Committee. Experiments were performed under Home Office licence PPL 70/9001.

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
RH2-09	SA185837	FL022989	Mutant	Sample groups
RH2-09	SA185837	FL022989	unlabelled	Treatment

Collection:

Collection ID:	CO002060
Collection Summary:	Spleens were harvested from WT, heterozygous or homozygous Fbxo7LacZ mice and processed to a single cell suspension. For n=2 of Fig. 3E, cells were incubated in RBC lysis buffer (eBioscience) for 5 minutes prior to centrifugation. For all other data, viable lymphocytes were separated with mouse Lympholyte® Cell Separation Media (Cedarlane Labs). CD4+ T cells were then isolated by negative selection using the MojoSort Mouse CD4 T Cell Isolation Kit (Biolegend). Isolated CD4+ T cells were seeded at 1x106/mL in RPMI supplemented with 10% FBS, 100 U/mL penicillin and streptomycin and 5 µM β-mercaptoethanol. To activate, cells were added to plates coated with 2 µg/mL α-CD3 (clone 145-2C11) and containing 2 µg/mL soluble α-CD28 (clone 37.51) and incubated for the indicated duration. Cell viability and activation were measured by flow cytometry by staining with antibodies to CD4-PE (clone GK1.5), CD25-PE/Cy7 (clone PC61), CD69-FITC (clone H1.2F3) and an eFluor™ 780 fixable viability dye (eBioscience) for 30 min at 4oC in the dark. Samples were analysed on a CytoFLEX S flow cytometer.
Sample Type:	T-cells

Treatment:

Treatment ID:	TR002079
Treatment Summary:	To activate, cells were added to plates coated with 2 µg/mL α-CD3 (clone 145-2C11) and containing 2 µg/mL soluble α-CD28 (clone 37.51) and incubated for the indicated duration. Cell viability and activation were measured by flow cytometry by staining with antibodies to CD4-PE (clone GK1.5), CD25-PE/Cy7 (clone PC61), CD69-FITC (clone H1.2F3) and an eFluor™ 780 fixable viability dye (eBioscience) for 30 min at 4oC in the dark. Samples were analysed on a CytoFLEX S flow cytometer. For metabolite profiling (Fig. 4C & Supplementary Fig. 3C), murine CD4+ T cells were isolated and activated in a 12 well plate for 48 hours. For 13C stable isotope tracing (Fig. 4D), murine CD4+ T cells were isolated and activated in a 12 well plate with culture media containing 2g/L D-Glucose-1,2-13C2 (Sigma) for 24 hours.

Treatment ID:

TR002079

Treatment Summary:

To activate, cells were added to plates coated with 2 µg/mL α-CD3 (clone 145-2C11) and containing 2 µg/mL soluble α-CD28 (clone 37.51) and incubated for the indicated duration. Cell viability and activation were measured by flow cytometry by staining with antibodies to CD4-PE (clone GK1.5), CD25-PE/Cy7 (clone PC61), CD69-FITC (clone H1.2F3) and an eFluor™ 780 fixable viability dye (eBioscience) for 30 min at 4oC in the dark. Samples were analysed on a CytoFLEX S flow cytometer. For metabolite profiling (Fig. 4C & Supplementary Fig. 3C), murine CD4+ T cells were isolated and activated in a 12 well plate for 48 hours. For 13C stable isotope tracing (Fig. 4D), murine CD4+ T cells were isolated and activated in a 12 well plate with culture media containing 2g/L D-Glucose-1,2-13C2 (Sigma) for 24 hours.

Sample Preparation:

Sampleprep ID:	SP002073
Sampleprep Summary:	To extract metabolites, cells were harvested, washed twice in PBS and resuspended in 200 μL ice cold metabolite extraction solution (50% LC–MS grade methanol, 30% LC-MS grade acetonitrile, 20% ultrapure water, 5 μM valine-d8 as internal standard) per 1x106 cells. Cells were incubated in a dry ice-methanol bath for 20 min, then at 4oC with shaking for 15 min. Samples were centrifuged at 13000 rpm for 20 min and the supernatant was collected into autosampler vials for LC-MS analysis.

Sampleprep ID:

SP002073

Sampleprep Summary:

To extract metabolites, cells were harvested, washed twice in PBS and resuspended in 200 μL ice cold metabolite extraction solution (50% LC–MS grade methanol, 30% LC-MS grade acetonitrile, 20% ultrapure water, 5 μM valine-d8 as internal standard) per 1x106 cells. Cells were incubated in a dry ice-methanol bath for 20 min, then at 4oC with shaking for 15 min. Samples were centrifuged at 13000 rpm for 20 min and the supernatant was collected into autosampler vials for LC-MS analysis.

Combined analysis:

Analysis ID	AN003237
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Thermo Dionex Ultimate 3000
Column	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	UNSPECIFIED
Units	arbitrary unit

Chromatography:

Chromatography ID:	CH002387
Chromatography Summary:	LC-MS chromatographic separation of metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A was 20 mM ammonium carbonate, 0.05% ammonium hydroxide; Solvent B was acetonitrile. The column oven and autosampler tray were held at 40°C and 4°C, respectively. The chromatographic gradient was run at a flow rate of 0.200 mL/min as follows: 0–2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-22.5 min: hold at 80% B.
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:	40
Flow Gradient:	0-2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-22.5 min: hold at 80% B.
Flow Rate:	0.200 mL/min
Solvent A:	100% water; 20 mM ammonium carbonate; 0.05% ammonium hydroxide
Solvent B:	100% acetonitrile
Chromatography Type:	HILIC

MS:

MS ID:	MS003010
Analysis ID:	AN003237
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The mass spectrometer was operated in full-scan, polarity-switching mode, with the spray voltage set to +4.5 kV/-3.5 kV, the heated capillary held at 320°C, and the auxiliary gas heater held at 280°C. The sheath gas flow was set to 25 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 0 units. HRMS data acquisition was performed in a range of m/z = 70–900, with the resolution set at 70,000, the AGC target at 1x106, and the maximum injection time (Max IT) at 120 ms. Metabolite identities were confirmed using two parameters: (1) precursor ion m/z was matched within 5 ppm of theoretical mass predicted by the chemical formula; (2) the retention time of metabolites was within 5% of the retention time of a purified standard run with the same chromatographic method. Chromatogram review and peak area integration were performed using the Thermo Fisher software Tracefinder (v.5.0). Correction for natural abundance was performed using the Accucor Package (v.0.2.3)
Ion Mode:	UNSPECIFIED