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MB Sample ID: SA079829
Local Sample ID: | MMV028038-20180530 |
Subject ID: | SU001214 |
Subject Type: | Cultured cells |
Subject Species: | Plasmodium falciparum |
Taxonomy ID: | 5833 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001214 |
Subject Type: | Cultured cells |
Subject Species: | Plasmodium falciparum |
Taxonomy ID: | 5833 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
MMV028038-20180530 | SA079829 | FL012233 | MMV028038, 2.5 hours | Drug treatment |
Collection:
Collection ID: | CO001208 |
Collection Summary: | Aspiration of 4 mL media, transfer of sample (1 mL) to 1.5 mL tubes, centrifugation, removal of supernatant, PBS wash, centrifugation, and extraction via 90% methanol with labelled aspartate. |
Collection Protocol Filename: | Metabolite_Extraction_for_LCMS_2017_Llinas.pdf |
Sample Type: | Cultured cells |
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: | TR001229 |
Treatment Summary: | Infected Red Blood cells were exposed to Antimalarial Compounds, associated with sample names. All samples were treated with 10xIC50 of a compound for 2.5 hours or left untreated for 2.5 hours. |
Treatment Protocol ID: | Metabolite_Extraction_for_LCMS_2017_Llinas |
Treatment Protocol Filename: | Metabolite_Extraction_for_LCMS_2017_Llinas.pdf |
Treatment: | Abiotic |
Treatment Compound: | ATQ, MMV009108, MMV019662, MMV028038 |
Treatment Route: | Addition to media |
Treatment Dose: | 10xIC50, 2-10xIC50 for archival data |
Treatment Dosevolume: | Always equal to or less than 10 uL per 5 mL sample |
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: | SP001222 |
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 |
Sample Spiking: | Labelled Aspartate, Chlorpropamide |
Combined analysis:
Analysis ID | AN001896 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Thermo Dionex Ultimate 3000 |
Column | Waters XSelect HSS T3 XP (100 x 2.1mm,2.5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Exactive Plus Orbitrap |
Ion Mode | NEGATIVE |
Units | Peak Area Post-Blank Subtraction |
Chromatography:
Chromatography ID: | CH001373 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Waters XSelect HSS T3 XP (100 x 2.1mm,2.5um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS001752 |
Analysis ID: | AN001896 |
Instrument Name: | Thermo Exactive Plus Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Blank subtraction, RSD cutoffs both by RSD per sample and pooled QCs to eliminate metabolites affected by time-dependency |
Ion Mode: | NEGATIVE |