Summary of Study ST002840
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 PR001779. The data can be accessed directly via it's Project DOI: 10.21228/M8RM7K 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 | ST002840 |
| Study Title | Collaborative role of YqgC and superoxide dismutase (MnSOD) in manganese intoxication: Replicate Experiment 1 |
| Study Type | Targeted MS Analysis |
| Study Summary | In this study, we are validating the mutual impact of yqgC and superoxide dismutase (MnSOD) deletion (YS strain) and resultant hypersensitivity to Manganese (Mn). Our genetic and physiological studies show that Mn intoxication is a result of distinct enzymatic vulnerabilities via alleviated expression of Mg-dependent, chorismate-utilizing enzymes of the menaquinone, siderophore, and tryptophan (MST) family (due to mismetalation). |
| Institute | Cornell University |
| Department | Medicine |
| Laboratory | Rhee Lab |
| Last Name | Soni |
| First Name | Vijay |
| Address | Weill Cornell Medical College, 413 E 69th St |
| vis2032@med.cornell.edu | |
| Phone | 9175391105 |
| Submit Date | 2023-08-28 |
| Num Groups | 10 |
| Total Subjects | 60 |
| Study Comments | NA |
| Publications | NA |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Chear Study | NA |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-09-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001779 |
| Project DOI: | doi: 10.21228/M8RM7K |
| Project Title: | Collaborative role of YqgC and superoxide dismutase (MnSOD) in manganese intoxication |
| Project Type: | LC-MS targettged analysis |
| Project Summary: | Bacterial metal ion homeostasis is strongly regulated by various metalloregulators. This project is focused on the role of yqgC-soda operon of B. subtilis in Manganese (Mn) ion metal homeostasis and the dependencies of these genes to maintain bacterial survival in the excess of Mn. |
| Institute: | Weill Cornell Medicine |
| Department: | Medicine |
| Laboratory: | Rhee Lab |
| Last Name: | Soni |
| First Name: | Vijay |
| Address: | 413 E 69TH STREET, Belfer Research Building, New York, New York, 10021, USA |
| Email: | vis2032@med.cornell.edu |
| Phone: | 9175391105 |
| Funding Source: | R35GM122461, NIAID:R25 AI140472 |
| Project Comments: | NA |
| Publications: | NA |
| Contributors: | Ankita J. Sachla, Vijay Soni, Yuanchan Luo, Kyu Y. Rhee, John D. Helmann |
Subject:
| Subject ID: | SU002950 |
| Subject Type: | Bacteria |
| Subject Species: | Bacillus subtilis |
| Taxonomy ID: | 1423 |
| Genotype Strain: | 168 |
| Age Or Age Range: | NA |
| Weight Or Weight Range: | NA |
| Height Or Height Range: | NA |
| Gender: | Not applicable |
| Cell Biosource Or Supplier: | NA |
| Cell Strain Details: | NA |
| Subject Comments: | NA |
| Cell Primary Immortalized: | NA |
| Cell Passage Number: | NA |
| Cell Counts: | NA |
| Species Group: | NA |
Factors:
Subject type: Bacteria; Subject species: Bacillus subtilis (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA307479 | PSb_Mn_Lys1 | mnePmneS_Mn_treated |
| SA307480 | PSa_Mn_Lys1 | mnePmneS_Mn_treated |
| SA307481 | PSc_Mn_Lys1 | mnePmneS_Mn_treated |
| SA307482 | PSa_UT_Lys1 | mnePmneS_untreated |
| SA307483 | PSc_UT_Lys1 | mnePmneS_untreated |
| SA307484 | PSb_UT_Lys1 | mnePmneS_untreated |
| SA307485 | Sc_Mn_Lys1 | sodA_Mn_treated |
| SA307486 | Sb_Mn_Lys1 | sodA_Mn_treated |
| SA307487 | Sa_Mn_Lys1 | sodA_Mn_treated |
| SA307488 | Sa_UT_Lys1 | sodA_untreated |
| SA307489 | Sc_UT_Lys1 | sodA_untreated |
| SA307490 | Sb_UT_Lys1 | sodA_untreated |
| SA307473 | WTc_Mn_Lys1 | WTCU1065_Mn_treated |
| SA307474 | WTb_Mn_Lys1 | WTCU1065_Mn_treated |
| SA307475 | WTa_Mn_Lys1 | WTCU1065_Mn_treated |
| SA307476 | WTb_UT_Lys1 | WTCU1065_untreated |
| SA307477 | WTa_UT_Lys1 | WTCU1065_untreated |
| SA307478 | WTc_UT_Lys1 | WTCU1065_untreated |
| SA307497 | Yc_Mn_Lys1 | yqgC_Mn_treated |
| SA307498 | Yb_Mn_Lys1 | yqgC_Mn_treated |
| SA307499 | Ya_Mn_Lys1 | yqgC_Mn_treated |
| SA307491 | YSb_Mn_Lys1 | yqgC-sodA_Mn_treated |
| SA307492 | YSa_Mn_Lys1 | yqgC-sodA_Mn_treated |
| SA307493 | YSc_Mn_Lys1 | yqgC-sodA_Mn_treated |
| SA307494 | YSc_UT_Lys1 | yqgC-sodA_untreated |
| SA307495 | YSa_UT_Lys1 | yqgC-sodA_untreated |
| SA307496 | YSb_UT_Lys1 | yqgC-sodA_untreated |
| SA307500 | Yb_UT_Lys1 | yqgC_untreated |
| SA307501 | Ya_UT_Lys1 | yqgC_untreated |
| SA307502 | Yc_UT_Lys1 | yqgC_untreated |
| Showing results 1 to 30 of 30 |
Collection:
| Collection ID: | CO002943 |
| Collection Summary: | All strains were grown in LB at 37 ˚C until 0.4 OD600 followed by 60 min treatment with or without 0.15 mM MnCl2 37 ˚C. Cells were pelleted and quenched by resuspending in chilled 0.6 ml of mixtures of acetonitrile:methanol:water (40:40:20). |
| Collection Protocol ID: | NA |
| Collection Protocol Filename: | NA |
| Collection Protocol Comments: | NA |
| Sample Type: | Bacterial cells |
| Collection Method: | NA |
| Collection Location: | NA |
| Collection Frequency: | NA |
| Collection Duration: | NA |
| Volumeoramount Collected: | NA |
| Storage Conditions: | -80℃ |
| Collection Vials: | Bead beating tubes |
| Storage Vials: | NA |
| Additives: | NA |
| Tissue Cell Identification: | NA |
| Tissue Cell Quantity Taken: | NA |
Treatment:
| Treatment ID: | TR002959 |
| Treatment Summary: | All strains were treated without (control group) or with (treated group) 0.15 mM of MnCl2 for 60 min at 37 ˚C. |
| Treatment Protocol ID: | NA |
| Treatment Protocol Filename: | NA |
| Treatment Protocol Comments: | NA |
| Treatment: | NA |
| Treatment Compound: | MnCl2 salt |
| Treatment Route: | Direct in bacterial culture |
| Treatment Dose: | 0.15 mM |
| Treatment Dosevolume: | NA |
| Treatment Doseduration: | NA |
| Treatment Vehicle: | Water |
| Cell Storage: | -80 |
| Cell Growth Container: | Flask |
| Cell Growth Config: | 200 rpm |
| Cell Growth Rate: | 40-60 min |
| Cell Inoc Proc: | NA |
| Cell Media: | LB Media |
| Cell Envir Cond: | NA |
| Cell Harvesting: | acetonitrile:methanol:water (40:40:20) |
| Cell Pct Confluence: | 0.4 OD600 |
| Cell Media Lastchanged: | NA |
Sample Preparation:
| Sampleprep ID: | SP002956 |
| Sampleprep Summary: | Samples were lysed using 0.1 mm Zirconia beads in a Precellys homogenizer. Lysed suspensions were centrifuged at 12,000 rpm for 8 min at 37 ˚C. Supernatants were passed through 0.22 um SpinX tube filter and flowthrough was collected for the LC-MS run. |
| Sampleprep Protocol ID: | NA |
| Sampleprep Protocol Filename: | NA |
| Sampleprep Protocol Comments: | NA |
| Processing Method: | NA |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Beat beating |
| Extract Enrichment: | NA |
| Extract Cleanup: | NA |
| Extract Storage: | 4℃ |
| Sample Resuspension: | NA |
| Sample Derivatization: | NA |
| Sample Spiking: | NA |
| Subcellular Location: | NA |
Combined analysis:
| Analysis ID | AN004647 | AN004648 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Normal phase | Normal phase |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Microsolv Diamond hydride (150 x 2.1mm,4um) | Microsolv Diamond hydride (150 x 2.1mm,4um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6220 TOF | Agilent 6220 TOF |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | Area under the curve | Area under the curve |
Chromatography:
| Chromatography ID: | CH003497 |
| Chromatography Summary: | Liquid chromatography (Agilent 1290 Infinity II) was used for the formic acid method. |
| Methods ID: | NA |
| Methods Filename: | NA |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Microsolv Diamond hydride (150 x 2.1mm,4um) |
| Column Pressure: | NA |
| Column Temperature: | 25 |
| Flow Gradient: | 0–2 min, 85% B; 3–5 min, 80% B; 6–7 min, 75%; 8–9 min, 70% B; 10–11 min, 50% B; 11–14 min 20% B; 14–24 min 5% B followed by a 10 min re-equilibration period at 85% B |
| Flow Rate: | 0.4 |
| Injection Temperature: | 25 |
| Solvent A: | Milli Q H2O + 0.2% Formic Acid |
| Solvent B: | Acetonitrile + 0.2% Formic Acid |
| Chromatography Type: | Normal phase |
| Solvent C: | NA |
| Chromatography ID: | CH003498 |
| Chromatography Summary: | Liquid chromatography (Agilent 1290 Infinity II) was used for the formic acid method. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Microsolv Diamond hydride (150 x 2.1mm,4um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0–2 min, 85% B; 3–5 min, 80% B; 6–7 min, 75%; 8–9 min, 70% B; 10–11 min, 50% B; 11–14 min 20% B; 14–24 min 5% B followed by a 10 min re-equilibration period at 85% B |
| Flow Rate: | 0.4 |
| Solvent A: | Milli Q H2O + 0.2% Formic Acid |
| Solvent B: | Acetonitrile + 0.2% Formic Acid |
| Chromatography Type: | Normal phase |
| Solvent C: | NA |
MS:
| MS ID: | MS004394 |
| Analysis ID: | AN004647 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Profinder B.08.00 Was used for the data analysis |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004395 |
| Analysis ID: | AN004648 |
| Instrument Name: | Agilent 6220 TOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Profinder B.08.00 Was used for the data analysis |
| Ion Mode: | POSITIVE |
