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MB Sample ID: SA164895
| Local Sample ID: | StrainsMetabs_WSB_1_8 |
| 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 |
Select appropriate tab below to view additional metadata details:
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:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| StrainsMetabs_WSB_1_8 | SA164895 | FL019713 | WSB/EiJ | Strain |
| StrainsMetabs_WSB_1_8 | SA164895 | FL019713 | 13 | SacDay |
| StrainsMetabs_WSB_1_8 | SA164895 | FL019713 | TRUE | Infected_yn |
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 |
