Return to study ST002698 main page
MB Sample ID: SA267158
| Local Sample ID: | Plasma_PIC_4 |
| Subject ID: | SU002801 |
| Subject Type: | Other organism |
| Subject Species: | Plasmodium berghei |
| Taxonomy ID: | 5823 |
| Genotype Strain: | ANKA |
| Age Or Age Range: | NA |
| Weight Or Weight Range: | NA |
| Height Or Height Range: | NA |
| Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002801 |
| Subject Type: | Other organism |
| Subject Species: | Plasmodium berghei |
| Taxonomy ID: | 5823 |
| Genotype Strain: | ANKA |
| Age Or Age Range: | NA |
| Weight Or Weight Range: | NA |
| Height Or Height Range: | NA |
| Gender: | Not applicable |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Plasma_PIC_4 | SA267158 | FL034976 | PIC | Extraction blank |
Collection:
| Collection ID: | CO002794 |
| Collection Summary: | C57BL/6J mice were purchased from the Animal Resource Centre (Perth, Australia). C57BL/6J.rag1−/− mice were bred at QIMR Berghofer Medical Research Institute. All mice were female between 6-12 weeks of age and were maintained under conventional conditions. Plasmodium berghei ANKA parasites constitutively expressing high-levels of eGFP (for RBC adoptive transfer), or luciferase (for establishing acute infection, although bioluminescence was not utilised), were sourced and used as previously reported12,16,17. PbA parasites were used after defrosting cryopreserved infected blood and a single in vivo passage in C57BL/6J mice. RBCs were collected from passage mice by cardiac puncture and used to infect with 105 pRBCs via lateral tail vein injection. |
| Sample Type: | infected Red Blood Cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002810 |
| Treatment Summary: | Mice were treated with Saline (0.9%; Baxter), Lipopolysaccharide (LPS; 0.75 mg/mL) (Sigma-Aldrich), CpG 1826 (0.25 mg/mL) (Sigma-Aldrich) or Polyriboinosinic:polyribocytidylic acid (Poly I:C; 2 mg/mL) (InvivoGen) via intraperitoneal injection (200 μL per mouse) using 26G needles, two hours prior to adoptive transfer of CFTR-labelled RBCs. |
Sample Preparation:
| Sampleprep ID: | SP002807 |
| Sampleprep Summary: | Two independent experiments were conducted, each with 6 mice per treatment group. Ice-cold butanol/methanol (1:1) containing 50 µg/mL antioxidant 2,6-di-tert-butyl-4-methylphenol (BHT) was added to each plasma sample, as well as a pooled quality control (QC) sample at 10x volume. Samples were vortexed for 10 seconds then snap frozen on dry ice. Thawed samples were sonicated for 15 minutes on ice, stored for 2 hours at -30°C, and then centrifuged for 15 minutes at 16,000×g (4°C). Supernatant was collected, aliquoted, dried down using a vacuum concentrator and stored at -80°C until LC/MS analysis. |
| Processing Storage Conditions: | 4℃ |
| Extraction Method: | MeOH/BuOH (1:1) |
| Extract Storage: | -80℃ |
| Sample Resuspension: | NA |
| Sample Derivatization: | NA |
Combined analysis:
| Analysis ID | AN004372 | AN004373 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
| Column | SeQuant ZIC-HILIC (150 x 4.6mm,3.5um) | SeQuant ZIC-HILIC (150 x 4.6mm,3.5um) |
| 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 | peak height | peak height |
Chromatography:
| Chromatography ID: | CH003278 |
| Chromatography Summary: | pHILIC chromatography pH9, 32 min run with posneg switching |
| Methods Filename: | Metabolomics_pHILIC_Parkville_v1.pdf |
| Instrument Name: | Thermo Dionex Ultimate 3000 RS |
| Column Name: | SeQuant ZIC-HILIC (150 x 4.6mm,3.5um) |
| Column Pressure: | 60 bar at starting conditions. 180 bar at %A |
| Column Temperature: | 25 C |
| Flow Gradient: | 0 min - 80%B, 15 min - 50%B, 18 min - 5%B, 21 min - 5%B, 24 min - 80%B, 32 min - 80%B |
| Flow Rate: | 0.3 ml/min |
| Injection Temperature: | 4 C |
| Sample Injection: | 10 uL |
| Solvent A: | 20 mM ammonium carbonate |
| Solvent B: | acetonitrile |
| Analytical Time: | 32 min |
| Capillary Voltage: | 4 kV |
| Oven Temperature: | 25 C |
| Washing Buffer: | syringe wash 50% IPA |
| Weak Wash Solvent Name: | 50% IPA |
| Strong Wash Volume: | 50% IPA |
| Sample Loop Size: | 25 uL |
| Sample Syringe Size: | 25 uL |
| Randomization Order: | yes |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS004120 |
| Analysis ID: | AN004372 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Acquired using XCalibur software (Thermo Scientific) |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 300 C |
| Capillary Voltage: | 4 kV |
| Collision Energy: | NA |
| Collision Gas: | NA |
| Dry Gas Flow: | 50 |
| Dry Gas Temp: | 120 |
| Ion Source Temperature: | 120 C |
| Ionization: | ESI |
| Mass Accuracy: | 3 ppm |
| Precursor Type: | [M+H]+ |
| Acquisition Parameters File: | Metabolomics_pHILIC_Parkville_v1.pdf |
| Analysis Protocol File: | PQMS3-MPMF-WIN-0501_LCMS_data_acquisition_for_untargeted_metabolomics_analysis.pdf |
| MS ID: | MS004121 |
| Analysis ID: | AN004373 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Acquired using XCalibur software (Thermo Scientific) |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 300 C |
| Capillary Voltage: | 3.5 kV |
| Collision Energy: | NA |
| Collision Gas: | NA |
| Dry Gas Flow: | 50 |
| Dry Gas Temp: | 120 |
| Ion Source Temperature: | 120 C |
| Ionization: | ESI |
| Mass Accuracy: | 3 ppm |
| Precursor Type: | [M-H]- |
| Acquisition Parameters File: | Metabolomics_pHILIC_Parkville_v1.pdf |
| Analysis Protocol File: | PQMS3-MPMF-WIN-0501_LCMS_data_acquisition_for_untargeted_metabolomics_analysis.pdf |
