Summary of study ST000546

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 PR000400. The data can be accessed directly via it's Project DOI: 10.21228/M8BS4F This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST000546
Study TitleMulti-omics based identification of specific biochemical changes associated with PfKelch13-mutant artemisinin resistant Plasmodium
Study TypeCell type comparison
Study SummaryTwo clonaly artemisinin resistant parasitised red blood cells (trophozoite stage) were compared with artemsinin sensitive parasitised red blood cells by metabolomics analysis.
Institute
Monash University
DepartmentMonash Institute of Pharmaceutical Sciences, Drug Delivery, Disposition and Dynamics
LaboratoryCreek lab
Last NameCreek
First NameDarren
Address381 Royal Parade, Parkville, Melbourne, VIC3052, Australia
EmailDarren.Creek@monash.edu
PhoneN/A
Submit Date2017-01-23
Num Groups4
Total Subjects13
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2017-07-10
Release Version1
Darren Creek Darren Creek
https://dx.doi.org/10.21228/M8BS4F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000400
Project DOI:doi: 10.21228/M8BS4F
Project Title:Multi-omics based identification of specific biochemical changes associated with PfKelch13-mutant artemisinin resistant Plasmodium falciparum
Project Summary:None
Institute:Monash University
Department:Monash Institute of Pharmaceutical Sciences, Drug Delivery, Disposition and Dynamics
Laboratory:Creek lab
Last Name:Creek
First Name:Darren
Address:381 Royal Parade, Parkville, Melbourne, VIC3052, Australia
Email:Darren.Creek@monash.edu
Phone:N/A
Funding Source:NHMRC

Subject:

Subject ID:SU000568
Subject Type:Cells
Subject Species:Plasmodium falciparum
Taxonomy ID:5833
Genotype Strain:Cam3.IIR539T (Cambodian isolate, artemisinin resistant) R1 | Cam3.IIC580Y (Cambodian isolate, artemisinin resistant) R2 | Cam3.IIrev (Cambodian isolate, artemisinin sensitive) S | uninfected red blood cells
Cell Strain Details:Artemisinin resistant strain (R1) | Artemisinin resistant strain (R2) | Artemisinin sensitive strain (S) | uninfected red blood cells
Cell Primary Immortalized:Primary | Primary | Primary | Primary
Cell Counts:5 x 10e7 per sample (purified infected cells) | 5 x 10e7 per sample (purified infected cells) | 5 x 10e7 per sample (purified infected cells) | 5 x 10e7 per sample
Species Group:Microorganism

Factors:

Subject type: Cells; Subject species: Plasmodium falciparum (Factor headings shown in green)

mb_sample_id local_sample_id Artemisinin resistant PfKelch13 mutation
SA028145R2_60exp3Resistant C580Y
SA028146R2_60exp2Resistant C580Y
SA028147R2_60exp1Resistant C580Y
SA028148R1_60exp2Resistant R539T
SA028149R1_60exp1Resistant R539T
SA028150R1_60exp3Resistant R539T
SA028151S_60exp3Sensitive WT
SA028152S_60exp1Sensitive WT
SA028153S_60exp2Sensitive WT
SA028154URBCS_exp4Uinfected red blood cells Control
SA028155URBCS_exp3Uinfected red blood cells Control
SA028156URBCS_exp2Uinfected red blood cells Control
SA028157URBCS_exp1Uinfected red blood cells Control
Showing results 1 to 13 of 13

Collection:

Collection ID:CO000562
Collection Summary:None
Sample Type:Cell
Collection Method:Plasmodium falciparum parasites (two clonal artemisnin resistant

Treatment:

Treatment ID:TR000582
Treatment Summary:None

Sample Preparation:

Sampleprep ID:SP000575
Sampleprep Summary:Metabolism was quenched by washing with ice cold PBS (1 mL). Cells were then pelleted by centrifugation (6000 xg for 3 min) and metabolites were extracted from 5 x 107 uninfected red blood cells and 5 x 107 parasitised red blood cells reticulocytes by addition of 140 µL methanol containing internal standards (CHAPS, CAPS, PIPES and TRIS; 1 µM) and left for 1 hour at 4 °C with automatic vortex. After mixing, cellular debris was removed by centrifugation (16,000 rpm for 10 mins) and the supernatant was kept at -20 °C prior to analysis.
Processing Method:Lysis with automatic vortex at 4°C
Processing Storage Conditions:On ice or 4°C
Extraction Method:Methanol
Extract Storage:-20°C
Sample Spiking:Internal standards (CHAPS, CAPS, PIPES and TRIS; all at 1 µM) mixed in extraction solvent
Cell Type:Artemisinin resistant and sensitive parasitised red blood cells and uninfected red blood cells

Combined analysis:

Analysis ID AN000832 AN000833
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column ZIC-pHILIC (Merck Sequant) column ZIC-pHILIC (Merck Sequant) column
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:CH000595
Chromatography Summary:Untargeted HILIC method
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:ZIC-pHILIC (Merck Sequant) column
Column Temperature:25°C
Flow Gradient:linear gradient -time, %B as follows: 0min- 80%, 15min- 50%, 18min- 5%, 21min- 5%, 24min- 80%, 32min- 80%.
Flow Rate:300 μL/min
Injection Temperature:4 °C
Internal Standard:internal standards (CHAPS, CAPS, PIPES and TRIS; all at 1 µM)
Sample Injection:10 μL
Solvent A:20 mM ammonium carbonate in water
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS000733
Analysis ID:AN000832
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
Capillary Temperature:300°C
Capillary Voltage:+50 V
Fragmentation Method:None
Spray Voltage:4kV
  
MS ID:MS000734
Analysis ID:AN000833
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
Capillary Temperature:300°C
Capillary Voltage:+50 V
Fragmentation Method:None
Spray Voltage:3.5kV
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