Summary of Study ST001775

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001129. The data can be accessed directly via it's Project DOI: 10.21228/M8RX1D This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST001775
Study Title	Plasma metabolomics of diverse mouse strains infected with Plasmodium chabaudi
Study Summary	To uncover links between metabolism and disease severity in murine malaria, we performed plasma metabolomics via Metabolon on eight inbred, Plasmodium chabaudi-infected mouse strains with diverse disease phenotypes. We sacrificed and collected plasma from >=3 mice per strain per day of acute infection alongside uninfected control mice (approximately days 5-12 depending on mouse strain). We collected disease severity data, e.g. weight loss, liver enzymes, and anemia, concurrently. Together, these data enable 1) a picture of strain-specific and conserved metabolic responses during acute malaria, and 2) a comparison between metabolic responses and disease severity.
Institute	Stanford University
Department	Microbiology & Immunology
Laboratory	David Schneider
Last Name	Schneider
First Name	David
Address	299 Campus Drive, Stanford, CA 94305
Email	dschneid@stanford.edu
Phone	650-724-8064
Submit Date	2021-04-11
Num Groups	8 mouse strains +/- Plasmodium infection
Total Subjects	369
Num Females	369
Analysis Type Detail	LC-MS
Release Date	2021-05-21
Release Version	1

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Project:

Project ID:	PR001129
Project DOI:	doi: 10.21228/M8RX1D
Project Title:	Plasma metabolomics of diverse mouse strains infected with Plasmodium chabaudi
Project Summary:	To uncover links between metabolism and disease severity in murine malaria, we performed plasma metabolomics via Metabolon on eight inbred, Plasmodium chabaudi-infected mouse strains with diverse disease phenotypes. We sacrificed and collected plasma from >=3 mice per strain per day of acute infection alongside uninfected control mice (approximately days 5-12 depending on mouse strain). We collected disease severity data, e.g. weight loss, liver enzymes, and anemia, concurrently. Together, these data enable 1) a picture of strain-specific and conserved metabolic responses during acute malaria, and 2) a comparison between metabolic responses and disease severity.
Institute:	Stanford University
Department:	Microbiology & Immunology
Laboratory:	David Schneider
Last Name:	Schneider
First Name:	David
Address:	299 Campus Drive
Email:	dschneid@stanford.edu
Phone:	650-724-8064

Subject:

Subject ID:	SU001852
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090
Genotype Strain:	C57BL/6 ; PWK/PhJ ; WSB/EiJ ; NZO/HILtJ ; A/J ; 129S1/SvImJ ; CAST/EiJ ; NOD/ShiLtJ
Age Or Age Range:	8-12 weeks
Gender:	Female
Animal Animal Supplier:	JAX (except C57BL/6, who came from Charles River)
Animal Housing:	standard
Animal Light Cycle:	standard
Animal Feed:	TEKLAD global
Animal Water:	standard

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Strain	SacDay	Infected_yn
SA164573	StrainsMetabs_129_1_34	129S1/SvImJ	10	TRUE
SA164574	StrainsMetabs_129_1_32	129S1/SvImJ	10	TRUE
SA164575	StrainsMetabs_129_1_33	129S1/SvImJ	10	TRUE
SA164576	StrainsMetabs_129_1_31	129S1/SvImJ	10	TRUE
SA164577	StrainsMetabs_129_1_30	129S1/SvImJ	10	TRUE
SA164578	StrainsMetabs_129_2_B6_2_30	129S1/SvImJ	11	FALSE
SA164579	StrainsMetabs_129_2_B6_2_31	129S1/SvImJ	11	FALSE
SA164580	StrainsMetabs_129_2_B6_2_20	129S1/SvImJ	11	TRUE
SA164581	StrainsMetabs_129_2_B6_2_18	129S1/SvImJ	11	TRUE
SA164582	StrainsMetabs_129_2_B6_2_16	129S1/SvImJ	11	TRUE
SA164583	StrainsMetabs_129_2_B6_2_17	129S1/SvImJ	11	TRUE
SA164584	StrainsMetabs_129_2_B6_2_19	129S1/SvImJ	11	TRUE
SA164585	StrainsMetabs_129_2_B6_2_25	129S1/SvImJ	12	TRUE
SA164586	StrainsMetabs_129_2_B6_2_21	129S1/SvImJ	12	TRUE
SA164587	StrainsMetabs_129_2_B6_2_22	129S1/SvImJ	12	TRUE
SA164588	StrainsMetabs_129_2_B6_2_24	129S1/SvImJ	12	TRUE
SA164589	StrainsMetabs_129_2_B6_2_23	129S1/SvImJ	12	TRUE
SA164590	StrainsMetabs_129_2_B6_2_2	129S1/SvImJ	3	TRUE
SA164591	StrainsMetabs_129_2_B6_2_27	129S1/SvImJ	3	TRUE
SA164592	StrainsMetabs_129_2_B6_2_1	129S1/SvImJ	3	TRUE
SA164593	StrainsMetabs_129_2_B6_2_7	129S1/SvImJ	4	TRUE
SA164594	StrainsMetabs_129_2_B6_2_8	129S1/SvImJ	4	TRUE
SA164595	StrainsMetabs_129_2_B6_2_6	129S1/SvImJ	4	TRUE
SA164596	StrainsMetabs_129_2_B6_2_13	129S1/SvImJ	5	TRUE
SA164597	StrainsMetabs_129_2_B6_2_11	129S1/SvImJ	5	TRUE
SA164598	StrainsMetabs_129_2_B6_2_12	129S1/SvImJ	5	TRUE
SA164599	StrainsMetabs_129_1_10	129S1/SvImJ	6	TRUE
SA164600	StrainsMetabs_129_1_9	129S1/SvImJ	6	TRUE
SA164601	StrainsMetabs_129_1_6	129S1/SvImJ	6	TRUE
SA164602	StrainsMetabs_129_1_7	129S1/SvImJ	6	TRUE
SA164603	StrainsMetabs_129_1_8	129S1/SvImJ	6	TRUE
SA164604	StrainsMetabs_129_1_17	129S1/SvImJ	7	FALSE
SA164605	StrainsMetabs_129_1_16	129S1/SvImJ	7	FALSE
SA164606	StrainsMetabs_129_1_12	129S1/SvImJ	7	TRUE
SA164607	StrainsMetabs_129_1_15	129S1/SvImJ	7	TRUE
SA164608	StrainsMetabs_129_1_14	129S1/SvImJ	7	TRUE
SA164609	StrainsMetabs_129_1_11	129S1/SvImJ	7	TRUE
SA164610	StrainsMetabs_129_1_13	129S1/SvImJ	7	TRUE
SA164611	StrainsMetabs_129_1_19	129S1/SvImJ	8	TRUE
SA164612	StrainsMetabs_129_1_21	129S1/SvImJ	8	TRUE
SA164613	StrainsMetabs_129_1_22	129S1/SvImJ	8	TRUE
SA164614	StrainsMetabs_129_1_20	129S1/SvImJ	8	TRUE
SA164615	StrainsMetabs_129_1_18	129S1/SvImJ	8	TRUE
SA164616	StrainsMetabs_129_1_28	129S1/SvImJ	9	FALSE
SA164617	StrainsMetabs_129_1_29	129S1/SvImJ	9	FALSE
SA164618	StrainsMetabs_129_1_25	129S1/SvImJ	9	TRUE
SA164619	StrainsMetabs_129_1_24	129S1/SvImJ	9	TRUE
SA164620	StrainsMetabs_129_1_26	129S1/SvImJ	9	TRUE
SA164621	StrainsMetabs_129_1_23	129S1/SvImJ	9	TRUE
SA164622	StrainsMetabs_129_1_27	129S1/SvImJ	9	TRUE
SA164623	StrainsMetabs_AJ_49	A/J	10	TRUE
SA164624	StrainsMetabs_AJ_48	A/J	10	TRUE
SA164625	StrainsMetabs_AJ_9	A/J	3	FALSE
SA164626	StrainsMetabs_AJ_8	A/J	3	FALSE
SA164627	StrainsMetabs_AJ_4	A/J	3	TRUE
SA164628	StrainsMetabs_AJ_5	A/J	3	TRUE
SA164629	StrainsMetabs_AJ_6	A/J	3	TRUE
SA164630	StrainsMetabs_AJ_10	A/J	4	TRUE
SA164631	StrainsMetabs_AJ_13	A/J	4	TRUE
SA164632	StrainsMetabs_AJ_14	A/J	4	TRUE
SA164633	StrainsMetabs_AJ_21	A/J	5	FALSE
SA164634	StrainsMetabs_AJ_20	A/J	5	FALSE
SA164635	StrainsMetabs_AJ_15	A/J	5	TRUE
SA164636	StrainsMetabs_AJ_16	A/J	5	TRUE
SA164637	StrainsMetabs_AJ_17	A/J	5	TRUE
SA164638	StrainsMetabs_AJ_24	A/J	6	TRUE
SA164639	StrainsMetabs_AJ_25	A/J	6	TRUE
SA164640	StrainsMetabs_AJ_26	A/J	6	TRUE
SA164641	StrainsMetabs_AJ_22	A/J	6	TRUE
SA164642	StrainsMetabs_AJ_23	A/J	6	TRUE
SA164643	StrainsMetabs_AJ_32	A/J	7	FALSE
SA164644	StrainsMetabs_AJ_33	A/J	7	FALSE
SA164645	StrainsMetabs_AJ_29	A/J	7	TRUE
SA164646	StrainsMetabs_AJ_28	A/J	7	TRUE
SA164647	StrainsMetabs_AJ_31	A/J	7	TRUE
SA164648	StrainsMetabs_AJ_27	A/J	7	TRUE
SA164649	StrainsMetabs_AJ_30	A/J	7	TRUE
SA164650	StrainsMetabs_AJ_37	A/J	8	TRUE
SA164651	StrainsMetabs_AJ_39	A/J	8	TRUE
SA164652	StrainsMetabs_AJ_35	A/J	8	TRUE
SA164653	StrainsMetabs_AJ_38	A/J	8	TRUE
SA164654	StrainsMetabs_AJ_34	A/J	8	TRUE
SA164655	StrainsMetabs_AJ_45	A/J	9	FALSE
SA164656	StrainsMetabs_AJ_44	A/J	9	FALSE
SA164657	StrainsMetabs_AJ_46	A/J	9	TRUE
SA164658	StrainsMetabs_AJ_40	A/J	9	TRUE
SA164659	StrainsMetabs_AJ_42	A/J	9	TRUE
SA164660	StrainsMetabs_AJ_41	A/J	9	TRUE
SA164661	StrainsMetabs_AJ_43	A/J	9	TRUE
SA164662	StrainsMetabs_129_2_B6_2_47	C57BL/6	10	TRUE
SA164663	StrainsMetabs_129_2_B6_2_50	C57BL/6	10	TRUE
SA164664	StrainsMetabs_129_2_B6_2_48	C57BL/6	10	TRUE
SA164665	StrainsMetabs_129_2_B6_2_46	C57BL/6	10	TRUE
SA164666	StrainsMetabs_129_2_B6_2_49	C57BL/6	10	TRUE
SA164667	StrainsMetabs_129_2_B6_2_70	C57BL/6	11	FALSE
SA164668	StrainsMetabs_129_2_B6_2_69	C57BL/6	11	FALSE
SA164669	StrainsMetabs_129_2_B6_2_52	C57BL/6	11	TRUE
SA164670	StrainsMetabs_129_2_B6_2_51	C57BL/6	11	TRUE
SA164671	StrainsMetabs_129_2_B6_2_55	C57BL/6	11	TRUE
SA164672	StrainsMetabs_129_2_B6_2_53	C57BL/6	11	TRUE

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Collection:

Collection ID:	CO001845
Collection Summary:	See protocol document for full study details. Between 3 and 5 infected mice of each strain were euthanized each day from days 3-12 post-infection for cross-sectional analysis. Because the WSB/EiJ strain experiences delayed peak infection severity relative to the other mouse strains in this study, 3 or 4 WSB/EiJ mice were euthanized each day from days 3-17 post-infection for cross-sectional analysis. For each mouse strain, 2 uninfected control animals were euthanized at baseline and generally on odd-numbered days between days 3-12 or 3-17 for WSB/EiJ mice. Euthanasia was performed using carbon dioxide asphyxiation in accordance with Stanford University and APLAC guidelines for humane euthanasia. Following euthanasia, blood was collected via cardiac puncture using 25Gx5/8IN tuberculin syringes (Fisher Scientific 14-841-34). Syringes were primed by filling the syringe barrel with 0.5M EDTA, pH 8.0 anticoagulant and dispensing all but 50uL. Collected blood was stored on ice in 1.5mL Eppendorf tubes for 15-45 minutes before spinning at 1,000xg at 4 degrees C for 5 minutes in a tabletop centrifuge. Plasma was frozen at -80C immediately, and thawed/re-frozen once to aliquot for downstream cytokine, metabolite, and liver enzyme analyses. 100uL of plasma was shipped to Metabolon (https://www.metabolon.com/, Durham, NC, USA), which performed a combination of gas and liquid chromatography with mass spectrometry (GC/LC-MS). Compounds were identified by comparing sample peaks to an internal Metabolon library of known and unknown compounds. Raw peak values were obtained using area-the-curve. Additional data normalizations were performed by Metabolon to account for sample dilutions and day-to-day variation in instrument performance.
Collection Protocol Filename:	strainsmetabs_methods_for_mw.docx
Sample Type:	Blood (plasma)

Treatment:

Treatment ID:	TR001865
Treatment Summary:	See protocol document for full study details. 2 female C57BL/6 mice were given intraperitoneal (i.p.) injections of 100uL frozen stock of P. chabaudi-infected red blood cells (iRBCs). When parasitemia reached 10-20% at 8-10 days post-infection, mice were euthanized and blood obtained via cardiac puncture. Blood was diluted to 105 iRBC / 100uL in Kreb’s saline with glucose (KSG) and administered i.p. to experimental animals at a dose of 105 iRBCs. https://www.nature.com/articles/nprot.2011.313 Control animals received 100uL of vehicle i.p. Only female mice 8-12 weeks of age were used for P. chabaudi experiments. Experiments were performed in multiple cohorts. Parasitemia was quantified via thin blood smear, methanol fixation, KaryoMAX Giemsa (GIBCO) staining, and manual microscope counting at 100X magnification. RBCs were quantified using a BD Accuri C6 Plus cytometer (see Longitudinal Infection monitoring). Longitudinal monitoring was performed as described previously (Torres et al. 2016, PLOS Biol, “Tracking Resilience to Infections by Mapping Disease Space”). For each mouse, baseline RBC, weight, body temperature, and blood glucose measurements were collected between 1 and 5 days prior to infection. In some cases, blood glucose was collected only at baseline sampling and on the day of sacrifice. Mice were restrained during sample collection using tail-access rodent restrainers (Stoelting Co.). Blood was collected from the tail vein by nicking the end of the tail with disinfected surgical scissors, and depositing the blood into EDTA-coated capillary tubes to prevent clotting. For total RBC quantitation, 2uL of blood was diluted in 1mL of cold 1x Hank’s Balanced Salt Solution (HBSS) and kept on ice until absolute RBC counts were obtained using forward and side scatter gates on a BD Accuri C6 Plus flow cytometer. To record body temperature, mice in the metabolic screen experiments were implanted with subcutaneous electronic temperature and ID transponders (IPTT-300 transponders, Bio Medic Data System, Inc) one week prior to infection. Mice were locally anesthetized using a 2% lidocaine solution (100 ug delivered per dose) prior to implantation. Temperature data was recorded using a DAS-7006/7 s reader (Bio Medic Data System, Inc). Subsequent to metabolic screen experiments, body temperatures were measured using a thermocouple thermometer and mouse rectal probe (World Precision Instruments, RET-3). Blood glucose measurements were obtained with 2uL of tail vein blood analyzed with a Bayer CONTOUR Blood Glucose Monitor and Test Strips. Post-infection sampling began on day 4 or 5 post-infection. Parasitemia values were obtained as detailed above. Parasite density is the number of iRBCs per microliter of blood, and is calculated by multiplying parasitemia by the number of total RBCs.
Treatment Protocol Filename:	strainsmetabs_methods_for_mw.docx

Sample Preparation:

Sampleprep ID:	SP001858
Sampleprep Summary:	See protocol document for full study details. Between 3 and 5 infected mice of each strain were euthanized each day from days 3-12 post-infection for cross-sectional analysis. Because the WSB/EiJ strain experiences delayed peak infection severity relative to the other mouse strains in this study, 3 or 4 WSB/EiJ mice were euthanized each day from days 3-17 post-infection for cross-sectional analysis. For each mouse strain, 2 uninfected control animals were euthanized at baseline and generally on odd-numbered days between days 3-12 or 3-17 for WSB/EiJ mice. Euthanasia was performed using carbon dioxide asphyxiation in accordance with Stanford University and APLAC guidelines for humane euthanasia. Following euthanasia, blood was collected via cardiac puncture using 25Gx5/8IN tuberculin syringes (Fisher Scientific 14-841-34). Syringes were primed by filling the syringe barrel with 0.5M EDTA, pH 8.0 anticoagulant and dispensing all but 50uL. Collected blood was stored on ice in 1.5mL Eppendorf tubes for 15-45 minutes before spinning at 1,000xg at 4 degrees C for 5 minutes in a tabletop centrifuge. Plasma was frozen at -80C immediately, and thawed/re-frozen once to aliquot for downstream cytokine, metabolite, and liver enzyme analyses. 100uL of plasma was shipped to Metabolon (https://www.metabolon.com/, Durham, NC, USA), which performed a combination of gas and liquid chromatography with mass spectrometry (GC/LC-MS). Compounds were identified by comparing sample peaks to an internal Metabolon library of known and unknown compounds. Raw peak values were obtained using area-the-curve. Additional data normalizations were performed by Metabolon to account for sample dilutions and day-to-day variation in instrument performance.
Sampleprep Protocol Filename:	strainsmetabs_methods_for_mw.docx

Combined analysis:

Analysis ID	AN002882
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Waters Acquity
Column	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE
Units	ion counts

Chromatography:

Chromatography ID:	CH002137
Chromatography Summary:	see protocol document (strainsmetabs_methods_for_mw.docx) for Metabolon workflow
Methods Filename:	strainsmetabs_methods_for_mw.docx
Instrument Name:	Waters Acquity
Column Name:	Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS002675
Analysis ID:	AN002882
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Proprietary analytical software for integration and peak picking. Units are scaled imputed ion counts, derived from raw ion counts and corrected by Metabolon to account for day-to-day variation in instrument performance. Directly from Metabolon: "Values for each sample are normalized by volume and dilution effect. ; Each biochemical in OrigScale is then rescaled to set the median equal to 1. ; Lastly, missing values are imputed with the minimum."
Ion Mode:	POSITIVE