Summary of study ST001074

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 PR000719. The data can be accessed directly via it's Project DOI: 10.21228/M8R38S This work is supported by NIH grant, U2C- DK119886.

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Study IDST001074
Study TitleOpen source discovery of starting points for next generation chemoprotective antimalarial drugs (Biofocus 1)
Study TypeDrug Exposure
Study SummaryMetabolic examination/confirmation of resistance mutations observed in study
Institute
Pennsylvania State University
DepartmentBMB
LaboratoryLlinás
Last NameOwen
First NameEdward
AddressW-122 Millennium Science Complex, Pollock Road, University Park, PA 16802
Emaileso5005@psu.edu
Phone(814) 867-3527
Submit Date2018-02-15
Analysis Type DetailLC-MS
Release Date2018-10-16
Release Version1
Edward Owen Edward Owen
https://dx.doi.org/10.21228/M8R38S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000719
Project DOI:doi: 10.21228/M8R38S
Project Title:Open source discovery of starting points for next generation chemoprotective antimalarial drugs (Biofocus 1)
Project Type:LC-MS Metabolomics
Project Summary:Hydrophilic LC-MS analysis of Biofocus 1 compounds as part of functional validation of publication.
Institute:Pennsylvania State University
Department:BMB
Laboratory:Llinás Laboratory
Last Name:Owen
First Name:Edward
Address:W-122 Millennium Science Complex, Pollock Road, University Park, PA 16802
Email:eso5005@psu.edu
Phone:Lab: (814) 867-3527
Funding Source:Bill & Melinda Gates Foundation
Project Comments:RAW files not submitted as untargeted analysis likely ongoing following publication

Subject:

Subject ID:SU001118
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:Plasmodium falciparum, 5833
Genotype Strain:3D7
Cell Counts:1x10^8 per technical replicate
Species Group:Plasmodium falciparum

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Drug Treatment conc.
SA072463ATQ-20170426Atovaquone 10 nM
SA072464ATQ-20170802Atovaquone 10 nM
SA072465ATQ-20170130Atovaquone 10 nM
SA072466ATQ-20170413Atovaquone 10 nM
SA072467ATQ-20170928Atovaquone 10 nM
SA072468ATQ-20171019Atovaquone 10 nM
SA072469ATQ-20170327Atovaquone 10 nM
SA072470ATQ-20170207Atovaquone 10 nM
SA072471ATQ-20170224Atovaquone 10 nM
SA072472ATQ-20170316Atovaquone 10 nM
SA072473ATQ-20170309Atovaquone 10 nM
SA072474MMV011772-20170928MMV011772 6040 nM
SA072475MMV1010248-20171019MMV1010248 18795 nM
SA072476MMV1068987-20171019MMV1068987 7931.5 nM
SA072477MMV1319550-20170207MMV1319550 9680 nM
SA072478MMV1319550-20170413MMV1319550 9680 nM
SA072479MMV1427995-20170130MMV1427995 1389 nM
SA072480MMV1427995-20170413MMV1427995 1389 nM
SA072481MMV1427995-20170224MMV1427995 1389 nM
SA072482MMV1431916-20170426MMV1431916 6320 nM
SA072483MMV1431916-20170207MMV1431916 6320 nM
SA072484MMV1432165-20170413MMV1432165 1070 nM
SA072485MMV1432165-20170224MMV1432165 1070 nM
SA072486MMV1432165-20170130MMV1432165 1070 nM
SA072487MMV1432711-20170802MMV1432711 860 nM
SA072488MMV1449124-20171019MMV1449124 482.6 nM
SA072489MMV1451822-20170207MMV1451822 560 nM
SA072490MMV1451822-20170327MMV1451822 560 nM
SA072491MMV1454442-20170413MMV1454442 1730 nM
SA072492MMV1454442-20170130MMV1454442 1730 nM
SA072493MMV1454442-20170224MMV1454442 1730 nM
SA072494MMV1490397-20171019MMV1490397 1250 nM
SA072495MMV1490397-20170426MMV1490397 1250 nM
SA072496MMV1490397-20170309MMV1490397 1250 nM
SA072497MMV1490405-20170316MMV1490405 1130 nM
SA072498MMV1490405-20170309MMV1490405 1130 nM
SA072499ND-20170426None (Control) N/A
SA072500ND-20170802None (Control) N/A
SA072501ND-20171019None (Control) N/A
SA072502ND-20170413None (Control) N/A
SA072503ND-20170928None (Control) N/A
SA072504ND-20170327None (Control) N/A
SA072505ND-20170207None (Control) N/A
SA072506ND-20170224None (Control) N/A
SA072507ND-20170309None (Control) N/A
SA072508ND-20170316None (Control) N/A
SA072509ND-20170130None (Control) N/A
Showing results 1 to 47 of 47

Collection:

Collection ID:CO001112
Collection Summary:Aspiration of 4 mL media, transfer of sample (1 mL containing infected red blood cells) to 1.5 mL tubes
Collection Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Sample Type:Parasite
Collection Method:Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes
Collection Location:Biological safety hood
Collection Frequency:once after 2.5 hours treatment
Collection Duration:Collection and extraction occurs in under 20 minutes per plate
Volumeoramount Collected:1 mL containing 1x10^8 infected cells
Storage Conditions:On ice
Collection Vials:1.5 mL eppendorf
Storage Vials:1.5 mL eppendorf

Treatment:

Treatment ID:TR001132
Treatment Summary:Infected Red Blood cells were exposed to Antimalarial Compounds, associated with sample names
Treatment Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Treatment:Drug Treatment
Treatment Compound:MMV1432165, MMV1451822, MMV1068987, MMV1490405, MMV1490397, MMV1449124, MMV1432711, MMV1454442, MMV1010248, MMV1319550, MMV1427995, MMV1431916, MMV011772
Treatment Route:Addition to media
Treatment Dose:10xIC50
Treatment Dosevolume:10xIC50
Treatment Doseduration:2.5 hours
Treatment Vehicle:Stocks kept in either DMSO or Water
Cell Storage:Temperature/Gas Mixture controlled incubator
Cell Growth Container:6-well plate
Cell Growth Config:5 mL per well, each with 1x10^8 cells
Cell Media:RPMI 1640 w/ Albumax, Gentamycin, Hypoxanthine, HEPES, Sodium Bicarbonate
Cell Harvesting:PBS Wash followed by 90% methanol extraction

Sample Preparation:

Sampleprep ID:SP001125
Sampleprep Summary:Samples washed in PBS, spun down, aspirated, extracted in 90% methanol with labelled aspartate, then dried, resuspended in water labelled with chlorpropamide
Sampleprep Protocol Filename:Metabolite_Extraction_for_LCMS_2017_Llinas.pdf
Processing Method:Wash, Lysis, Drying, resuspension
Processing Storage Conditions:On ice
Extraction Method:90% Methanol Lysis
Extract Storage:-80℃
Sample Resuspension:100 uL water with chlorpropamide

Combined analysis:

Analysis ID AN001756
Analysis type MS
Chromatography type Normal phase
Chromatography system Thermo Dionex Ultimate 3000
Column Phenomenex Synergi Hydro RP (100 x 2mm, 2.5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap
Ion Mode NEGATIVE
Units Average Peak Area

Chromatography:

Chromatography ID:CH001240
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Synergi Hydro RP (100 x 2mm, 2.5um)
Chromatography Type:Normal phase

MS:

MS ID:MS001624
Analysis ID:AN001756
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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