Summary of Study ST001149
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 PR000768. The data can be accessed directly via it's Project DOI: 10.21228/M8DH49 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001149 |
| Study Title | Plasmodium Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis |
| Study Type | Drug Exposure |
| Study Summary | Metabolic examination/confirmation of resistance mutations and GFP tagging observed in study |
| Institute | Pennsylvania State University |
| Department | BMB |
| Laboratory | Llinás Laboratory |
| Last Name | Llinás |
| First Name | Manuel |
| Address | W-122 Millennium Science Complex, Pollock Road |
| eso5005@psu.edu | |
| Phone | 8148673527 |
| Submit Date | 2019-02-15 |
| Raw Data Available | Yes |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-05-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000768 |
| Project DOI: | doi: 10.21228/M8DH49 |
| Project Title: | Plasmodium Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis |
| Project Type: | LC-MS Metabolomics |
| Project Summary: | Hydrophilic LC-MS analysis of PfNCR1 Targeting compounds as part of functional validation of publication |
| Institute: | Pennsylvania State University |
| Department: | BMB |
| Laboratory: | Llinás Laboratory |
| Last Name: | Llinás |
| First Name: | Manuel |
| Address: | W-122 Millennium Science Complex, Pollock Road, University Park, PA 16802 |
| Email: | manuel@psu.edu |
| Phone: | Office: (814) 867-3444, Lab: (814) 867-3527 |
| Publications: | Plasmodium Niemann-Pick Type C1-Related Protein is a Druggable Target Required for Parasite Membrane Homeostasis |
| Contributors: | Eva S. Istvan, Sudipta Das, Suyash Bhatnagar, Josh R. Beck, Edward Owen, Manuel Llinás, Suresh M. Ganesan, Jacquin C. Niles, Elizabeth A. Winzeler, Akhil B. Vaidya, Daniel E. Goldberg |
Subject:
| Subject ID: | SU001214 |
| Subject Type: | Cultured cells |
| Subject Species: | Plasmodium falciparum |
| Taxonomy ID: | 5833 |
| Species Group: | Unicellular parasites |
Factors:
Subject type: Cultured cells; Subject species: Plasmodium falciparum (Factor headings shown in green)
| mb_sample_id | local_sample_id | Drug treatment |
|---|---|---|
| SA079821 | ATQ-20180530 | Atovaquone, 2.5 hours |
| SA079822 | ATQ-MB2 | Atovaquone, 2.5 hours |
| SA079823 | ATQ-MB1 | Atovaquone, 2.5 hours |
| SA079824 | ATQ-20181025 | Atovaquone, 2.5 hours |
| SA079825 | MMV009108-MB2 | MMV009108, 2.5 hours |
| SA079826 | MMV009108-20180530 | MMV009108, 2.5 hours |
| SA079827 | MMV019662-MB1 | MMV019662, 2.5 hours |
| SA079828 | MMV019662-20180530 | MMV019662, 2.5 hours |
| SA079829 | MMV028038-20180530 | MMV028038, 2.5 hours |
| SA079830 | MMV028038-20181025 | MMV028038, 2.5 hours |
| SA079831 | ND-MB2 | Untreated, 2.5 hours |
| SA079832 | ND-20181025 | Untreated, 2.5 hours |
| SA079833 | ND-20180530 | Untreated, 2.5 hours |
| SA079834 | ND-MB1 | Untreated, 2.5 hours |
| Showing results 1 to 14 of 14 |
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 |
