Summary of Study ST003281
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 PR002033. The data can be accessed directly via it's Project DOI: 10.21228/M8TN7J This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003281 |
| Study Title | Phosphate availability conditions caspofungin tolerance, capsule attachment and titan cell formation in Cryptococcus neoformans |
| Study Type | Metabolomics and lipidomics |
| Study Summary | There is a pressing need for new antifungal drugs to treat invasive fungal diseases. Unfortunately, the echinocandin drugs that are fungicidal against other important fungal pathogens are ineffective against Cryptococcus neoformans, the causative agent of life-threatening meningoencephalitis in immunocompromised people. Contributing mechanisms for echinocandin tolerance are emerging with connections to calcineurin signaling, the cell wall, and membrane composition. In this context, we discovered that a defect in phosphate uptake impairs the tolerance of C. neoformans to the echinocandin caspofungin. |
| Institute | University of British Columbia |
| Department | Life Sciences Institute |
| Last Name | Alcazar Magana |
| First Name | Armando |
| Address | 2350 Health Sciences Mall |
| armando.alcazarmagana@ubc.ca | |
| Phone | 5416097172 |
| Submit Date | 2024-06-12 |
| Num Groups | 8 |
| Total Subjects | 28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-06-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002033 |
| Project DOI: | doi: 10.21228/M8TN7J |
| Project Title: | Phosphate availability conditions caspofungin tolerance, capsule attachment and titan cell formation in Cryptococcus neoformans |
| Project Summary: | There is a pressing need for new antifungal drugs to treat invasive fungal diseases. Unfortunately, the echinocandin drugs that are fungicidal against other important fungal pathogens are ineffective against Cryptococcus neoformans, the causative agent of life-threatening meningoencephalitis in immunocompromised people. Contributing mechanisms for echinocandin tolerance are emerging with connections to calcineurin signaling, the cell wall, and membrane composition. In this context, we discovered that a defect in phosphate uptake impairs the tolerance of C. neoformans to the echinocandin caspofungin. |
| Institute: | Life Sciences Institute, The University of British Columbia |
| Last Name: | Alcazar Magana |
| First Name: | Armando |
| Address: | 2350 Health Sciences Mall |
| Email: | armando.alcazarmagana@ubc.ca |
| Phone: | 5416097172 |
Subject:
| Subject ID: | SU003401 |
| Subject Type: | Fungi |
| Subject Species: | Cryptococcus neoformans |
Factors:
Subject type: Fungi; Subject species: Cryptococcus neoformans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment | Sample source |
|---|---|---|---|---|
| SA355149 | H99-0_A | H99 | 0 | Cells |
| SA355150 | H99-0_B | H99 | 0 | Cells |
| SA355151 | H99-0_C | H99 | 0 | Cells |
| SA355152 | H99-250_C | H99 | 250 | Cells |
| SA355153 | H99-250_B | H99 | 250 | Cells |
| SA355154 | H99-250_A | H99 | 250 | Cells |
| SA355155 | H99-iron-20Pi-24h_A | H99 | H99-iron-20Pi-24h | Cells |
| SA355156 | H99-iron-20Pi-24h_D | H99 | H99-iron-20Pi-24h | Cells |
| SA355157 | H99-iron-20Pi-24h_C | H99 | H99-iron-20Pi-24h | Cells |
| SA355158 | H99-iron-20Pi-24h_B | H99 | H99-iron-20Pi-24h | Cells |
| SA355159 | H99-iron-20Pi-6h_A | H99 | H99-iron-20Pi-6h | Cells |
| SA355160 | H99-iron-20Pi-6h_B | H99 | H99-iron-20Pi-6h | Cells |
| SA355161 | H99-iron-20Pi-6h_C | H99 | H99-iron-20Pi-6h | Cells |
| SA355162 | H99-iron-20Pi-6h_D | H99 | H99-iron-20Pi-6h | Cells |
| SA355163 | H99-iron-24h_A | H99 | H99-iron-24h | Cells |
| SA355164 | H99-iron-24h_D | H99 | H99-iron-24h | Cells |
| SA355165 | H99-iron-24h_C | H99 | H99-iron-24h | Cells |
| SA355166 | H99-iron-24h_B | H99 | H99-iron-24h | Cells |
| SA355167 | H99-iron-6h_D | H99 | H99-iron-6h | Cells |
| SA355168 | H99-iron-6h_C | H99 | H99-iron-6h | Cells |
| SA355169 | H99-iron-6h_B | H99 | H99-iron-6h | Cells |
| SA355170 | H99-iron-6h_A | H99 | H99-iron-6h | Cells |
| SA355171 | H99-no iron-20Pi-6h_C | H99 | H99-no iron-20Pi-6h | Cells |
| SA355172 | H99-no iron-20Pi-6h_D | H99 | H99-no iron-20Pi-6h | Cells |
| SA355173 | H99-no iron-20Pi-6h_A | H99 | H99-no iron-20Pi-6h | Cells |
| SA355174 | H99-no iron-20Pi-6h_B | H99 | H99-no iron-20Pi-6h | Cells |
| SA355175 | H99-no iron-6h_B | H99 | H99-no iron-6h | Cells |
| SA355176 | H99-no iron-6h_D | H99 | H99-no iron-6h | Cells |
| SA355177 | H99-no iron-6h_A | H99 | H99-no iron-6h | Cells |
| SA355178 | H99-no iron-6h_C | H99 | H99-no iron-6h | Cells |
| SA355179 | QC3 | H99 | QC | Cells |
| SA355180 | QC5 | H99 | QC | Cells |
| SA355181 | QC4 | H99 | QC | Cells |
| SA355182 | QC1 | H99 | QC | Cells |
| SA355183 | QC2 | H99 | QC | Cells |
| SA355184 | Pho-0_A | Pho | 0 | Cells |
| SA355185 | Pho-0_B | Pho | 0 | Cells |
| SA355186 | Pho-0_C | Pho | 0 | Cells |
| SA355187 | Pho-250_A | Pho | 250 | Cells |
| SA355188 | Pho-250_B | Pho | 250 | Cells |
| SA355189 | Pho-250_C | Pho | 250 | Cells |
| SA355190 | QCL3 | QC | QC | Cells |
| SA355191 | QCL1 | QC | QC | Cells |
| SA355192 | QCL2 | QC | QC | Cells |
| Showing results 1 to 44 of 44 |
Collection:
| Collection ID: | CO003394 |
| Collection Summary: | The analysis was performed with cells grown overnight in YPD, transferred to MM at 30°C, and normalized to an OD600 of 2 with 0 mM or 250 mM Pi. After 24 h of incubation, 2 ml of cells were transferred (normalized to an OD600 of 2) into a 2 mL microcentrifuge tube. For metabolomics, cells were grown overnight in YPD, transferred into LIM (with 2.5 mM Pi) with iron (using dH2O instead of low iron water) for 24 h. 5х107 cells were transferred into LIM (low iron, low Pi), LIM (low iron, 20 mM Pi), LIM (iron, low Pi) and LIM (iron, 20 mM Pi) for 6h. 3.5х107 cells were collected into a 2 mL microcentrifuge tube. Cells were centrifuged at 13,000 rpm, 4oC for 10 min, washed three times with ice-cold nanopure water. Lipid extraction was performed using a biphasic system of cold methanol, methyltert-butyl ether (MTBE), and H2O, as described with some modifications (Matyash, et al., 2008) |
| Sample Type: | Fungal cells |
Treatment:
| Treatment ID: | TR003410 |
| Treatment Summary: | The analysis was performed with cells grown overnight in YPD, transferred to MM at 30°C, and normalized to an OD600 of 2 with 0 mM or 250 mM Pi. |
Sample Preparation:
| Sampleprep ID: | SP003408 |
| Sampleprep Summary: | Lipid extraction was performed using a biphasic system of cold methanol, methyltert-butyl ether (MTBE), and H2O, as described with some modifications (Matyash, et al., 2008). |
Combined analysis:
| Analysis ID | AN005375 | AN005376 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Bruker Impact II | Bruker Impact II |
| Column | Agilent InfinityLab Poroshell 120 HILIC-Z column (2.7 µm particle size, 150 x 2.1 mm) | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Bruker Impact HD | Bruker Impact HD |
| Ion Mode | NEGATIVE | NEGATIVE |
| Units | Rel Abundance | Rel Abundance |
Chromatography:
| Chromatography ID: | CH004074 |
| Chromatography Summary: | A novel method optimized for highly polar compounds was used to analyze samples using Hydrophilic Interaction Liquid Chromatography (HILIC) |
| Instrument Name: | Bruker Impact II |
| Column Name: | Agilent InfinityLab Poroshell 120 HILIC-Z column (2.7 µm particle size, 150 x 2.1 mm) |
| Column Temperature: | 30 |
| Flow Gradient: | the initial condition of 90% B was held for 2 minutes, followed by a linear gradient to 40% B over 6 minutes, then maintained at 40% B for 2 minutes, returned to 90% B over 1.1 minutes, and equilibrated for 4.9 minutes, resulting in a total run time of 16 minutes |
| Flow Rate: | 0.3 ml/min |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium acetate; 5 µM medronic acid |
| Solvent B: | 90% acetonitrile/10% water ; 0.1% formic acid; 10 mM ammonium acetate; 5 µM medronic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004075 |
| Chromatography Summary: | Separation of compounds was achieved using a multigradient method on an Acquity CSH |
| Instrument Name: | Bruker Impact II |
| Column Name: | Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | 0 min 15% B; 0–2 min 30% B; 2–2.5 min 50% B; 2.5–12 min 80% B; 12–12.5 min 99% B; 12.5–13.5 min 99% B; 13.5–13.7 min 15% B; 13.7-17 min 15% B. |
| Flow Rate: | 0.5 ml/min |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005104 |
| Analysis ID: | AN005375 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw data processing of metabolites employed Progenesis QI™ (V3.0.7600.27622) software with the METLIN™ plugin (V1.0.7642.33805) |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005105 |
| Analysis ID: | AN005376 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Raw data processing of metabolites employed Progenesis QI™ (V3.0.7600.27622) software with the METLIN™ plugin (V1.0.7642.33805) |
| Ion Mode: | NEGATIVE |
