Summary of Study ST000515

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 PR000384. The data can be accessed directly via it's Project DOI: 10.21228/M8DP41 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000515
Study TitleMetabolomics of longitudinal plasma samples from Macaca mulatta infected with Plasmodium cynomolgi B strain.
Study TypeLongitudinal parasite infection and treatment of multiple individuals
Study SummaryATTENTION: The dataset package associated with this study is out of date. Please refer to https://www.ebi.ac.uk/metabolights/MTBLS517 for the latest and final version of all files. Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for parasitological, clinical, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug Artemether was subcuratively administered selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs Primaquine and Chloroquine were administered to all remaining subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Plasma samples were acquired every other day from capillary blood and during seven-time point collections of venous blood. Supplemental files, including a ReadMe with additional experimental details, all raw data, and analytical metadata, are provided as part of this submission.
Institute
Emory University
DepartmentSchool of Medicine, Vaccine Center at Yerkes
Last NameGalinski
First NameMary
AddressEmory University, 954 Gatewood Rd, Atlanta, GA 30329
Emailmahpic@emory.edu
PhoneN/A
Submit Date2016-11-23
Total Subjects5
Study CommentsMalaria Host Pathogen Interaction Center Experiment 04, 5 subjects 286 samples. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC). These results are a product of a consortium of researchers known as the Malaria Host Pathogen Interaction Center (MaHPIC). For more information on the MaHPIC, please visit http://www.systemsbiology.emory.edu/ . Within the MaHPIC, these data were collected as part of 'Experiment 04' (E04). To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp . This page will be updated as datasets are released to the public.
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2017-07-10
Release Version1
Mary Galinski Mary Galinski
https://dx.doi.org/10.21228/M8DP41
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000384
Project DOI:doi: 10.21228/M8DP41
Project Title:The Malaria Host-Pathogen Interaction Center (MaHPIC)
Project Type:Systems Biology
Project Summary:The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program supported by an NIH/NIAID contract (# HHSN272201200031C; see http://www.systemsbiology.emory.edu/index.html). The MaHPIC generates many data types (e.g., metabolomics, functional genomics, lipidomics, proteomics, clinical, parasitological, immune response) and mathematical models, to iteratively test and develop hypotheses related to the complex host-parasite dynamics in the course of malaria in non-human primates, and metabolomics data via collaborations with investigators conducting clinical studies in malaria endemic countries, with the overarching goal of better understanding human disease, pathogenesis, and immunity. Curation and maintenance of all data and metadata are the responsibility of the MaHPIC: Mary Galinski mary.galinski@emory.edu (MaHPIC Program Director), Jessica Kissinger jkissinger@uga.edu (MaHPIC Co-Program Director), Alberto Moreno alberto.moreno@emory.edu (MaHPIC Co-Program Director), and Ebru Karpuzoglu ekarpuzoglu@emory.edu (MaHPIC Scientific Project Manager)
Institute:Emory University
Department:School of Medicine, Vaccine Center at Yerkes
Last Name:Galinski
First Name:Mary
Address:Emory University, 954 Gatewood Rd, Atlanta, GA 30329
Email:mgalins@emory.edu
Phone:N/A
Funding Source:NIAID Contract: # HHSN272201200031C

Subject:

Subject ID:SU000537
Subject Type:Animal
Subject Species:Macaca mulatta
Taxonomy ID:9544
Age Or Age Range:N/A| N/A| ~3years| ~3years| ~3years| ~3years| ~3years
Weight Or Weight Range:N/A| N/A| 6.05 kg| 6.05 kg| 6.05 kg| 6.05 kg| 6.05 kg
Gender:Male| Male| Male| Male| Male| Male| Male
Subject Comments:Transfusion Donor| Reference Animal| Experimental Subject|Experimental Subject| Experimental Subject| Experimental Subject| Experimental Subject
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Macaca mulatta (Factor headings shown in green)

mb_sample_id local_sample_id Gender Prior Infection Days since Inoculation
SA0267601975092Male None -1
SA0267611975086Male None -1
SA0267621975080Male None -1
SA0267631975125Male None -1
SA0267641975020Male None -1
SA0267651979579Male None 1
SA0267661979551Male None 1
SA0267671979561Male None 1
SA0267681979546Male None 1
SA0267691979556Male None 1
SA0267702058598Male None 104
SA0267712058603Male None 104
SA0267722058593Male None 104
SA0267732058588Male None 104
SA0267742060792Male None 106
SA0267752060782Male None 106
SA0267762060797Male None 106
SA0267772060787Male None 106
SA0267781986957Male None 11
SA0267791986947Male None 11
SA0267801986942Male None 11
SA0267811986962Male None 11
SA0267821986952Male None 11
SA0267831988270Male None 13
SA0267841988255Male None 13
SA0267851988260Male None 13
SA0267861988250Male None 13
SA0267871988265Male None 13
SA0267881990896Male None 15
SA0267891990901Male None 15
SA0267901990911Male None 15
SA0267911990916Male None 15
SA0267921990906Male None 15
SA0267931991821Male None 17
SA0267941991841Male None 17
SA0267951991836Male None 17
SA0267961991831Male None 17
SA0267971991826Male None 17
SA0267981991880Male None 18
SA0267991993046Male None 19
SA0268001993026Male None 19
SA0268011993036Male None 19
SA0268021993031Male None 19
SA0268031993041Male None 19
SA0268041995832Male None 20
SA0268051995844Male None 20
SA0268061995910Male None 21
SA0268071996024Male None 21
SA0268081996019Male None 21
SA0268091996029Male None 21
SA0268101995922Male None 21
SA0268111998663Male None 23
SA0268121998668Male None 23
SA0268131998957Male None 23
SA0268141998658Male None 23
SA0268151998648Male None 23
SA0268161999114Male None 25
SA0268171999129Male None 25
SA0268181999119Male None 25
SA0268191999124Male None 25
SA0268201999443Male None 26
SA0268211999442Male None 26
SA0268221999441Male None 26
SA0268231999440Male None 26
SA0268242003641Male None 27
SA0268252003636Male None 27
SA0268262003626Male None 27
SA0268272003631Male None 27
SA0268282005641Male None 29
SA0268292005631Male None 29
SA0268302005646Male None 29
SA0268312005636Male None 29
SA0268321981033Male None 3
SA0268331981038Male None 3
SA0268341981028Male None 3
SA0268351981043Male None 3
SA0268361981023Male None 3
SA0268372005900Male None 31
SA0268382005895Male None 31
SA0268392005905Male None 31
SA0268402005890Male None 31
SA0268412006389Male None 33
SA0268422006384Male None 33
SA0268432006379Male None 33
SA0268442006374Male None 33
SA0268452008343Male None 35
SA0268462008338Male None 35
SA0268472008333Male None 35
SA0268482008328Male None 35
SA0268492010130Male None 37
SA0268502010125Male None 37
SA0268512010135Male None 37
SA0268522010120Male None 37
SA0268532010684Male None 39
SA0268542010679Male None 39
SA0268552010674Male None 39
SA0268562010689Male None 39
SA0268572012632Male None 41
SA0268582012642Male None 41
SA0268592012627Male None 41
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 286

Collection:

Collection ID:CO000531
Collection Summary:Every Other Day Collection|Time Point 1 - Baseline: Uninfected control for each NHP.|Time Point 2 - Peak of infection: Peak of infection determined by clinical and parasitological assessment for each NHP. The time point is intended to characterize the host immune response and capture multi-omics data during the peak of parasitemias when the NHP is experiencing clinical signs of disease that may be severe or non-severe. NHPs were monitored, and clinical interventions were performed as necessary. Otherwise, NHPs self-resolved infection.|Time Point 3 - Post-Peak of Infection: Observations 7 days after peak infection.|Time Point 4 - 1st Relapse Peak of Infection: This time point tested expectations of a mild drop in hemoglobin levels and low parasitemias relative to peak infection arising from activation of hypnozoites. |Time Point 5 - Post-Peak of 1st Relapse Infection: Inter-relapse interval. |Time Point 6 - 2nd Relapse Peak of Infection: Same goal as time point 4 for 2nd relapse.|Time Point 7 - Post-Peak of 2nd Relapse Infection: Observations on NHP response after a second relapse infection.
Sample Type:Whole blood
Collection Method:Ear Prick|Intravenous|Intravenous|Intravenous|Intravenous|Intravenous|Intravenous|Intravenous
Collection Time:Every Other Day|Once|Once|Once|Once|Once|Once|Once
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000551
Treatment Summary:Plasmodium Cynomolgi Strain B Sporozoites Inoculation
Treatment:Biotic
Treatment Route:Injection

Sample Preparation:

Sampleprep ID:SP000544
Sampleprep Summary:aliquots of 65ul sample were mixed with 130ul acetonitrile and 3.25ul internal standard. Keep on ice and vortex every 15 minutes. Centrifuge for 10 minutes at 13.2rpm and 4C. Using a pipette, 130ul of supernatant was removed and placed into autosampler vials for the mass spectrometer.
Sampleprep Protocol Filename:Metab_Sample_Preparation_Plasma_serum_v1_May_17_2013.docx
E4_E3_E18_E23_E24_E25_MalariaCore_Metabolomics_SOP_v1_6October2016.docx
Processing Method:Precipitation of protein, centrifuge, and remove supernatant
Processing Storage Conditions:on ice
Extraction Method:1:2 sample:acetonitrile
Extract Storage:Pipette supernatant into autosampler vials for mass spectrometer
Sample Spiking:C18 standards: Caffeine and Diethyl-toluamide. Stable isotopes: [13C6]-D-glucose, [15N]-indole, [1,2-13C2]-palmitic acid, [15N,13C5]-L-methionine, [2-15N]-L-lysine dihydrochloride, [15N]-choline chloride, [13C5]-L-glutamic acid, [13C7]-benzoic acid, [15N]-L-tyrosine, [15N2]-uracil, [3,4-13C2]-cholesterol, [3,3-13C2]-cystine, [trimethyl-13C3]-caffeine, [U-13C5, U-15N2]-L-glutamine.

Combined analysis:

Analysis ID AN000788 AN000789
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo QExactive Thermo QExactive
Column Higgins C18 (100 x 2.1mm,5um) Higgins C18 (100 x 2.1mm,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 intensity peak intensity

Chromatography:

Chromatography ID:CH000565
Chromatography Summary:untargeted chromatography (C18 column)
Methods Filename:Metab_Orbitrap_Setup_v1_May_17_2013.docx
Chromatography Comments:Thermo QExactive coupled to CTC PAL HTC Accela1-TMO autosampler
Instrument Name:Thermo QExactive
Column Name:Higgins C18 (100 x 2.1mm,5um)
Column Pressure:200 Bar (max)
Column Temperature:30
Flow Gradient:A%: 0-10mins = 5%; B%: 0-2mins = 35%, 2-7mins = gradient to 95%, 7-10mins = 95%; C%: 0-2mins = 60%, 2-7mins = gradient to 0%, 7-10mins = 0%
Flow Rate:0-2mins = 350 μL/min, 2-7mins = gradient to 400 μL/min, 7-10mins = 400 μL/min
Injection Temperature:4C
Internal Standard:Caffeine, Diethyl-toluamide
Internal Standard Mt:1.5 min; 6-6.6 min
Sample Injection:10μL
Sampling Cone:ESI: HESI probe with S-lens combination
Solvent A:100% water; 0.2% formic acid
Solvent B:100% acetonitrile
Analytical Time:10 minutes
Capillary Voltage:4.6 kV
Oven Temperature:45C
Running Voltage:4.6 kV
Weak Wash Solvent Name:H20 with 10% methanol
Weak Wash Volume:20μL
Chromatography Type:Reversed phase

MS:

MS ID:MS000695
Analysis ID:AN000788
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:250
Capillary Voltage:4.45
Collision Gas:N2
Gas Pressure:50 PSI
Ionization:electrospray ionization
Mass Accuracy:5 PPM
Source Temperature:48
Spray Voltage:3.5
Atom Gun Current:1000000
Dataformat:.raw,.cdf
Probe Tip:HESI
Resolution Setting:120,000
Scan Range Moverz:85-1275
Analysis Protocol File:Metabolomics_Core_Data_Analysis.docx
  
MS ID:MS000696
Analysis ID:AN000789
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:250
Capillary Voltage:4.45
Collision Gas:N2
Gas Pressure:50 PSI
Ionization:electrospray ionization
Mass Accuracy:5 PPM
Source Temperature:48
Spray Voltage:3.5
Atom Gun Current:1000000
Dataformat:.raw,.cdf
Probe Tip:HESI
Resolution Setting:120,000
Scan Range Moverz:85-1275
Analysis Protocol File:Metabolomics_Core_Data_Analysis.docx
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