Summary of study ST001298

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 PR000879. The data can be accessed directly via it's Project DOI: 10.21228/M82M47 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001298
Study TitleMetabolome Profiling of Synechococcus elongatus PCC 11801 strains engineered for Succinate Production
Study TypeMeasurement of relative metabolite pools of wild type and engineered Synechococcus elongatus PCC 11801 strains using Isotopic Ratio Method
Study SummaryExperiments to measure relative metabolite pools of wild type Synechococcus elongatus PCC 11801 and its recombinants producing succinate. The wild type and the engineered strains producing succinate were cultivated at 1% CO2 and their metabolome data was collected in three biological and three technical replicates (n=9). The study aims to find metabolomics changes between the wild type and the engineered to identify potential rate-limiting steps that be used as targets for improved production.
Institute
Indian Institute of Technology Bombay
DepartmentDepartment of Chemical Engineering
LaboratoryBio systems Engineering Lab
Last NameWangikar
First NamePramod P
AddressDepartment of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India - 400076
Emailwangikar@iitb.ac.in
Phone22254215
Submit Date2020-01-03
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2020-07-05
Release Version1
Pramod P Wangikar Pramod P Wangikar
https://dx.doi.org/10.21228/M82M47
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000879
Project DOI:doi: 10.21228/M82M47
Project Title:Metabolome Profiling of Synechococcus elongatus PCC 11801 strains engineered for Succinate Production
Project Type:Measurement of relative metabolite pools of wild type and engineered Synechococcus elongatus PCC 11801 strains
Project Summary:Experiments to measure relative metabolite pools of wild type Synechococcus elongatus PCC 11801 and its recombinants producing succinate. The wild type and the engineered strains producing succinate were cultivated at 1% CO2 and their metabolome data was collected in three biological and three technical replicates (n=9). The study aims to find metabolomics changes between the wild type and the engineered to identify potential rate-limiting steps that be used as targets for improved production.
Institute:Indian Institute of Technology Bombay
Department:Department of Chemical Engineering
Laboratory:Bio systems Engineering Lab
Last Name:Wangikar
First Name:Pramod P
Address:Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India - 400076
Email:wangikar@iitb.ac.in
Phone:+91 (22) 2576 7232
Funding Source:Department of Biotechnology (DBT), PAN-IIT Centre for Bioenergy (Grant No: BT/EB/PAN IIT/2012)

Subject:

Subject ID:SU001372
Subject Type:Bacteria
Subject Species:Synechococcus
Taxonomy ID:2219813
Genotype Strain:Synechococcus elongatus PCC 11801

Factors:

Subject type: Bacteria; Subject species: Synechococcus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA094196SA3 BR3-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094197SA3 BR3-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094198SA3 BR2-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094199SA3 BR3-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094200SA3 BR2-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094201SA3 BR2-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094202SA3 BR1-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094203SA3 BR1-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094204SA3 BR1-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR
SA094205SA7 BR2-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094206SA7 BR1-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094207SA7 BR1-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094208SA7 BR2-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094209SA7 BR3-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094210SA7 BR3-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094211SA7 BR2-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094212SA7 BR1-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094213SA7 BR3-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD Pcpcb300 PEPC SmR , DDOP62_03790 Prbcl400 gltA Prbcl400 SBPase/FBPase KanR
SA094214SA2 BR1-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094215SA2 BR1-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094216SA2 BR3-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094217SA2 BR3-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094218SA2 BR3-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094219SA2 BR2-3△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094220SA2 BR2-1△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094221SA2 BR2-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094222SA2 BR1-2△DOP62_03525 PpsbaI OgdA PpsbaIII SsaD SmR
SA094178WT EP BR2-2Wild type
SA094179WT EP BR2-3Wild type
SA094180WT EP BR3-1Wild type
SA094181WT EP BR2-1Wild type
SA094182WT EP BR1-3Wild type
SA094183WT BR1-1Wild type
SA094184WT EP BR1-1Wild type
SA094185WT EP BR1-2Wild type
SA094186WT EP BR3-3Wild type
SA094187WT EP BR3-2Wild type
SA094188WT BR2-1Wild type
SA094189WT BR1-3Wild type
SA094190WT BR1-2Wild type
SA094191WT BR2-3Wild type
SA094192WT BR2-2Wild type
SA094193WT BR3-3Wild type
SA094194WT BR3-2Wild type
SA094195WT BR3-1Wild type
Showing results 1 to 45 of 45

Collection:

Collection ID:CO001367
Collection Summary:The experiment was conducted in a shaker maintained at a temperature of 38°C, 1% CO2, and 120 rpm. The cells were grown in 100 ml shake flasks with 20 ml culture volume and the samples for metabolomics analysis were collected at a metabolic steady-state (OD 730 nm = 0.6). Samples were quenched with methanol and extracted using the methanol-chloroform-water method. Extracts were stored at -80°C till LCMS analysis. LCMS analysis was done in the negative ion mode using information-dependent acquisition (IDA) method.
Sample Type:Bacterial cells
Collection Tube Temp:4 degree centrigrade

Treatment:

Treatment ID:TR001387
Treatment Summary:The metabolites were extracted using a methanol-chloroform-water method described in the "Metabolite Extraction Protocol" file of the collection data.

Sample Preparation:

Sampleprep ID:SP001380
Sampleprep Summary:One aliquot of the metabolite extract of each sample were reconstituted in 100µL 50:50 methanol-water and filtered using nylon syringe filters to remove any particulate matter. The metabolite extract of each test sample was mixed with equal volume of an extract of the PCC 11801 WT biomass that is fully labeled with 13C isotopic carbon by growing for ~5 generations in the presence of NaH13CO3 in modified BG-11 medium. 13C-labeled biomass of PCC 11801 that acted as an internal standard. The injection volume was 6 µL. The peak areas corresponding to the 12C and 13C monoisotopic peak for the metabolites of interest were quantified using MultiQuant 3.0.1 (SCIEX, Framingham, MA). The relative quantification of metabolites was done using isotopic ratio method by normalizing area under the peak for monoisotopic m/z of a particular metabolite by its respective highest possible isotopologue present in the internal standard giving area ratio.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002162
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column Phenomenex Synergi Hydro RP 100 A (100 x 2mm, 2.5um)
MS Type ESI
MS instrument type QTOF
MS instrument name ABI Sciex 5600+ TripleTOF
Ion Mode NEGATIVE
Units Area Ratio

Chromatography:

Chromatography ID:CH001580
Instrument Name:Shimadzu 20AD
Column Name:Phenomenex Synergi Hydro RP 100 A (100 x 2mm, 2.5um)
Flow Gradient:The gradient method used is as follows: 0% B (0.01 min), 0% B (2 min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min), 90% B (20.5 min), 0% B (22 min), and 0% B (30 min)
Flow Rate:0.3 mL/minute
Solvent A:10 mM tributylamine + 15mM acetic acid in water
Solvent B:100% Methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS002011
Analysis ID:AN002162
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The peak areas corresponding to the 12C and 13C monoisotopic peak for the metabolites of interest were quantified using MultiQuant 3.0.1 (SCIEX, Framingham, MA). The relative quantification of metabolites was done using isotopic ratio method by normalizing area under the peak for monoisotopic m/z of a particular metabolite by its respective highest possible isotopologue present in the internal standard giving area ratio.
Ion Mode:NEGATIVE
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