Summary of study ST001080

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 PR000723. The data can be accessed directly via it's Project DOI: 10.21228/M87384 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 IDST001080
Study TitleDynamic labeling of intracellular metabolites in PCC 7002
Study TypeTimecourse experiment
Study SummaryThe experiment was conducted in a reactor at a metabolic steady state (OD 730 nm = 0.8). 13C labeled sodium bicarbonate was used as a tracer. Tracer concentration was 1 g/L. After the introduction of the tracer, the samples were collected at time point : 0, 60, 120, 180 and 240 secs. Samples were quenched with methanol and extracted using methanol-chloroform-water method. Extracts were stored at -80 degree C till LCMS analysis.
Institute
Indian Institute of Technology Bombay
DepartmentDepartment of Chemical Engineering
LaboratoryBio systems Engineering Lab
Last NameWangikar
First NamePramod
AddressPowai
Emailwangikar@iit.ac.in
Phone2225767232
Submit Date2018-10-18
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2019-08-01
Release Version1
Pramod Wangikar Pramod Wangikar
https://dx.doi.org/10.21228/M87384
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000723
Project DOI:doi: 10.21228/M87384
Project Title:13C Labeling Analysis of Synechococcus sp. PCC 7002
Project Type:13C tracing in intracellular metabolites of PCC 7002
Project Summary:An experiment conducted for Metabolic Flux Analysis of wild-type cyanobacterium Synechococcus sp. PCC 7002
Institute:Indian Institute of Technology Bombay
Department:Department of Chemical Engineering
Laboratory:Bio systems Engineering Lab
Last Name:Wangikar
First Name:Pramod
Address:IIT Bombay
Email:wangikar@iitb.ac.in
Phone:2225767232
Funding Source:Department of Biotechnology (DBT), PAN-IIT Centre for Bioenergy

Subject:

Subject ID:SU001124
Subject Type:Bacteria
Subject Species:Synechococcus sp. PCC 7002
Taxonomy ID:1131
Genotype Strain:Synechococcus

Factors:

Subject type: Bacteria; Subject species: Synechococcus sp. PCC 7002 (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA072837PCC 7002 180 SEC REP 2Wild type
SA072838PCC 7002 240 SEC REP 1Wild type
SA072839PCC 7002 240 SEC REP 2Wild type
SA072840PCC 7002 180 SEC REP 1Wild type
SA072841PCC 7002 120 SEC REP 2Wild type
SA072842PCC 7002 0 SEC REP 2Wild type
SA072843PCC 7002 60 SEC REP 1Wild type
SA072844PCC 7002 60 SEC REP 2Wild type
SA072845PCC 7002 120 SEC REP 1Wild type
SA072846PCC 7002 0 SEC REP 1Wild type
Showing results 1 to 10 of 10

Collection:

Collection ID:CO001118
Collection Summary:The experiment was conducted in a reactor at a metabolic steady state (OD 730 nm = 0.8). 13C labeled sodium bicarbonate was used as a tracer. Tracer concentration was 1 g/L. After the introduction of the tracer, 15 mL of the culture were collected at time point : 0, 60, 120, 180 and 240 secs. Samples were quenched with methanol and extracted using methanol-chloroform-water method. Extracts were stored at -80 degree C till LCMS analysis. LCMS analysis was done in negative ion mode using information dependent aquisition (IDA) method.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR001138
Treatment Summary:The metabolites were extracted using a methanol-chloroform-water method described in the "Metabolite Extraction Protocol_PCC 7002" file of the collection data.

Sample Preparation:

Sampleprep ID:SP001131
Sampleprep Summary:The metabolite extracts of different collected samples were reconstituted in 100 μL of 50/50 methanol-water mixture and filtered before injecting on LC/MS. Injection volume was 10 μL.

Combined analysis:

Analysis ID AN001763
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column Phenomenex Synergi Hydro RP (100 x 2mm, 2.5um)
MS Type ESI
MS instrument type Triple TOF
MS instrument name ABI Sciex 5600+ TripleTOF
Ion Mode NEGATIVE
Units Peak Area

Chromatography:

Chromatography ID:CH001246
Instrument Name:Shimadzu 20AD
Column Name:Phenomenex Synergi Hydro RP (100 x 2mm, 2.5um)
Flow Gradient:0% B (0 min), 0% B (2min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min), 90% B (20.5 min) and 0% B (22 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:MS001630
Analysis ID:AN001763
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
Ion Mode:NEGATIVE
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