Summary of Study ST002841

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.

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Study IDST002841
Study TitleCollaborative role of YqgC and superoxide dismutase (MnSOD) in manganese intoxication: Replicate Experiment 2
Study TypeTargeted MS Analysis
Study SummaryIn 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
DepartmentMedicine
LaboratoryRhee Lab
Last NameSoni
First NameVijay
AddressWeill Cornell Medical College, 413 E 69th St
Emailvis2032@med.cornell.edu
Phone9175391105
Submit Date2023-08-28
Num Groups10
Total Subjects60
Study CommentsNA
PublicationsNA
Raw Data AvailableYes
Raw Data File Type(s)mzML
Chear StudyNA
Analysis Type DetailLC-MS
Release Date2023-09-21
Release Version1
Vijay Soni Vijay Soni
https://dx.doi.org/10.21228/M8RM7K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU002951
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
SA307509PSe_Mn_Lys2mnePmneS_Mn_treated
SA307510PSd_Mn_Lys2mnePmneS_Mn_treated
SA307511PSf_Mn_Lys2mnePmneS_Mn_treated
SA307512PSd_UT_Lys2mnePmneS_untreated
SA307513PSf_UT_Lys2mnePmneS_untreated
SA307514PSe_UT_Lys2mnePmneS_untreated
SA307515Sf_Mn_Lys2sodA_Mn_treated
SA307516Se_Mn_Lys2sodA_Mn_treated
SA307517Sd_Mn_Lys2sodA_Mn_treated
SA307518Sd_UT_Lys2sodA_untreated
SA307519Sf_UT_Lys2sodA_untreated
SA307520Se_UT_Lys2sodA_untreated
SA307503WTf_Mn_Lys2WTCU1065_Mn_treated
SA307504WTe_Mn_Lys2WTCU1065_Mn_treated
SA307505WTd_Mn_Lys2WTCU1065_Mn_treated
SA307506WTe_UT_Lys2WTCU1065_untreated
SA307507WTd_UT_Lys2WTCU1065_untreated
SA307508WTf_UT_Lys2WTCU1065_untreated
SA307527Yf_Mn_Lys2yqgC_Mn_treated
SA307528Ye_Mn_Lys2yqgC_Mn_treated
SA307529Yd_Mn_Lys2yqgC_Mn_treated
SA307521YSe_Mn_Lys2yqgC-sodA_Mn_treated
SA307522YSd_Mn_Lys2yqgC-sodA_Mn_treated
SA307523YSf_Mn_Lys2yqgC-sodA_Mn_treated
SA307524YSf_UT_Lys2yqgC-sodA_untreated
SA307525YSd_UT_Lys2yqgC-sodA_untreated
SA307526YSe_UT_Lys2yqgC-sodA_untreated
SA307530Ye_UT_Lys2yqgC_untreated
SA307531Yd_UT_Lys2yqgC_untreated
SA307532Yf_UT_Lys2yqgC_untreated
Showing results 1 to 30 of 30

Collection:

Collection ID:CO002944
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:TR002960
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:SP002957
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 AN004649 AN004650
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:CH003499
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:CH003500
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:MS004396
Analysis ID:AN004649
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:MS004397
Analysis ID:AN004650
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
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