Summary of Study ST000326
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 PR000256. The data can be accessed directly via it's Project DOI: 10.21228/M8PS35 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000326 |
| Study Title | Role of medium in bacterial growth (HILIC chromatography) |
| Study Summary | Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2014-11-25 |
| Num Groups | 4 |
| Total Subjects | 38 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-01-27 |
| Release Version | 2 |
| Release Comments | Updated study design factors |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000256 |
| Project DOI: | doi: 10.21228/M8PS35 |
| Project Title: | Role of medium in bacterial growth |
| Project Summary: | Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | U24DK097154 |
Subject:
| Subject ID: | SU000346 |
| Subject Type: | Bacterial cells |
| Subject Species: | Bacteria |
| Species Group: | Microorganism |
Factors:
Subject type: Bacterial cells; Subject species: Bacteria (Factor headings shown in green)
| mb_sample_id | local_sample_id | labeltype |
|---|---|---|
| SA014716 | SA012 | A |
| SA014717 | SA013 | A |
| SA014718 | SA014 | A |
| SA014719 | SA015 | A |
| SA014720 | SA016 | A |
| SA014721 | SA017 | A |
| SA014722 | SA018 | A |
| SA014723 | SA019 | A |
| SA014724 | SA001 | E |
| SA014725 | SA010 | E |
| SA014726 | SA011 | E |
| SA014727 | SA002 | E |
| SA014728 | SA003 | E |
| SA014729 | SA004 | E |
| SA014730 | SA005 | E |
| SA014731 | SA006 | E |
| SA014732 | SA007 | E |
| SA014733 | SA008 | E |
| SA014734 | SA009 | E |
| Showing results 1 to 19 of 19 |
Collection:
| Collection ID: | CO000340 |
| Collection Summary: | - |
| Sample Type: | spent culture supernatant |
Treatment:
| Treatment ID: | TR000360 |
| Treatment Summary: | There are 2 treatments. Each sample is a supernatant from a different bacterial strain grown in culture.There are a total of 17 strains, 10 of which are grown in one type of medium and 7 are grown in another type of medium. Supernatants from the 2 types of media are also submitted for analysis. |
| Treatment Protocol Filename: | StudyDesign_NadirMahmood_072914.pdf |
Sample Preparation:
| Sampleprep ID: | SP000354 |
| Sampleprep Summary: | 1. After quenching the cells add 1 X 106 dried cells to 1.5 ml eppendorff tube. 2. Place the eppendorf tube with cells on dry ice for 20 minutes or til the cells are completely frozen and ice for 20 minutes, till they are completely thawed. Repeat this step twice. 3. Add 1ml of extraction solvent which has been pre-chilled using the ThermoElectron Neslab RTE 740 cooling bath set to -20°C. to the ependorff tube with cells. 4. Repeat step 2 twice with the extraction solvent. 5. Vortex the sample for 10s and shake for 5min at 4°C using the Orbital Mixing Chilling/Heating plate. Centrifuge samples for 2min at 14000 rcf using the centrifuge Eppendorf 5415 D. 6. Aliquot two 500µL portions of the supernatant. One for analysis and one for backup. Store one aliquot in the -20°C freezer as a backup. 7. Evaporate one 500µL aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. 8. Submit to derivatization |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Mammalian_Tissue_Samples.pdf |
Combined analysis:
| Analysis ID | AN000519 | AN000520 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Unspecified | Unspecified |
| Column | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
Chromatography:
| Chromatography ID: | CH000364 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_HILIC_QTOF_MS.pdf |
| Instrument Name: | Unspecified |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Column Pressure: | 200-700 bar |
| Column Temperature: | 45 C |
| Flow Gradient: | 100% B to 30% B |
| Flow Rate: | 0.4 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 3 uL |
| Solvent A: | 100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3 |
| Solvent B: | 95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate, pH 3 |
| Analytical Time: | 14 min |
| Capillary Voltage: | 4500 |
| Time Program: | 16.75 min |
| Weak Wash Solvent Name: | 1:1 ACN:H2O |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | 1:1 ACN:H2O |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS000455 |
| Analysis ID: | AN000519 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
| MS ID: | MS000456 |
| Analysis ID: | AN000520 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
