Summary of study ST001180

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 PR000792. The data can be accessed directly via it's Project DOI: 10.21228/M89M4D This work is supported by NIH grant, U2C- DK119886.

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Study IDST001180
Study TitleMetabolome Profiling of Synechococcus elogatus PCC 11802
Study TypeQuantitative Metabolomics
Study SummaryMetabolomics Analysis of a novel freshwater cyanobacterium, Synechococcus elongatus PCC 11802 isolated by us from Powai Lake, Mumbai, India. PCC 11802 cells were grown under ambient and 1% CO2 conditions and metabolomics data was collected in three biological replicates and two technical replicates (n=6). The study aims to find metabolomics changes in this cyanobacterium at elevated CO2 levels.
Institute
Indian Institute of Technology Bombay
DepartmentDepartment of Chemical Engineering
LaboratoryBiosystems Engineering Lab
Last NameWangikar
First NamePramod P
AddressPowai
Emailwangikar@iitb.ac.in
Phone+91 (22) 2576 7232
Submit Date2019-05-07
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2020-05-09
Release Version1
Pramod P Wangikar Pramod P Wangikar
https://dx.doi.org/10.21228/M89M4D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000792
Project DOI:doi: 10.21228/M89M4D
Project Title:Metabolome Analysis of Synechococcus elongatus PCC 11802
Project Type:Metabolomics
Project Summary:Metabolomics Analysis of a novel freshwater cyanobacterium, Synechococcus elongatus PCC 11802 isolated by us from Powai Lake, Mumbai, India. PCC 11802 cells were grown under ambient and 1% CO2 conditions and metabolomics data was collected in three biological replicates and two technical replicates (n=6). The study aims to find metabolomics changes in this cyanobacterium at elevated CO2 levels.
Institute:Indian Institute of Technology Bombay
Department:Department of Chemical Engineering
Laboratory:Biosystems Engineering Lab
Last Name:Wangikar
First Name:Pramod
Address:Room No. 136, Biosystems Engineering Laboratory, Mumbai, Maharashtra, 400076, India
Email:wangikar@iitb.ac.in
Phone:2225764215
Funding Source:DBT-PAN IIT Center for Bioenergy (Grant No: BT/EB/PAN IIT/2012)

Subject:

Subject ID:SU001246
Subject Type:Bacteria
Subject Species:Synechococcus elongatus PCC 11802
Taxonomy ID:1131

Factors:

Subject type: Bacteria; Subject species: Synechococcus elongatus PCC 11802 (Factor headings shown in green)

mb_sample_id local_sample_id Conditions
SA081616PCC 11802 1 PERCENT CO2 R31% CO2
SA081617PCC 11802 1 PERCENT CO2 R21% CO2
SA081618PCC 11802 1 PERCENT CO2 R11% CO2
SA081619PCC 11802 AMBIENT CO2 R2Ambient CO2
SA081620PCC 11802 AMBIENT CO2 R3Ambient CO2
SA081621PCC 11802 AMBIENT CO2 R1Ambient CO2
Showing results 1 to 6 of 6

Collection:

Collection ID:CO001240
Collection Summary:The PCC 11802 was grown under ambient and 1% CO2 conditions in triplicates in shake flasks at 200 uE light intensity, 38 degrees C temperature, 120 rpm. The samples were collected in exponential phase (OD730 = 0.6).The metabolites were extracted using methanol-chloroform-water method as described in "Metabolite Extraction Protocol" file. The samples were stored in a -80 degrees C deep freezer until analyzed using LCMS.
Sample Type:Cultured cells

Treatment:

Treatment ID:TR001261
Treatment Summary:The metabolites were extracted using a methanol-chloroform-water method described in the "Metabolite Extraction" file of the collection data.

Sample Preparation:

Sampleprep ID:SP001254
Sampleprep Summary:The metabolite extracts of different collected samples were reconstituted in 100 μL of 50/50 methanol-water mixture. An equal amount of fully 13C-labeled biomass extract from cyanobacterium Synechococcus elongatus PCC 11801 was added as internal standard. The mixture is vortexed. The samples are filtered through syringe filters. Injection volume was 6 uL.

Combined analysis:

Analysis ID AN001958
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:CH001419
Instrument Name:Shimadzu 20AD
Column Name:Phenomenex Synergi Hydro RP 100 A (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:MS001813
Analysis ID:AN001958
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Data Acquisition was done using IDA method with MS/MS trigerred for top 10 abundant precursor ions. Cycle time = 1s
Ion Mode:NEGATIVE
Collision Energy:-30
Ion Source Temperature:450
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