Summary of study ST001302

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 PR000883. The data can be accessed directly via it's Project DOI: 10.21228/M8JM4K This work is supported by NIH grant, U2C- DK119886.

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Study IDST001302
Study TitleMetabolome Profiling of a Fast-growing Cyanobacterium Synechococcus elongatus PCC 11801 under Diurnal Cycle
Study TypeMeasurement of relative metabolite pools under diurnal cycle using isotopic ratio method
Study SummaryExperiments were carried out by growing Synechococcus elongatus PCC 11801 cells in multicultivators designed to provide sinusoidal light. The period was 14:10 (light-dark). The samples for metabolomics analysis were collected in the second diurnal cycle at an interval of 6 hours starting from 25th hour (25, 31, 37 and 43 hours). The light intensity amplitude was 600 µmole photons.m-2. s-1. Additionally samples were also collected using cells grown under continuous light illumination of 600 µmole photons.m-2. s-1 to compare the difference in metabolite levels compared to that in the diurnal cycle.
Institute
Indian Institute of Technology Bombay
DepartmentDepartment of Chemical Engineering
LaboratoryBiosystems Engineering Lab
Last NameWangikar
First NamePramod P
AddressDepartment of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India - 400076
Emailwangikar@iitb.ac.in
Phone+91 (22) 2576 7232 (o)
Submit Date2020-01-06
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2020-10-11
Release Version1
Pramod P Wangikar Pramod P Wangikar
https://dx.doi.org/10.21228/M8JM4K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000883
Project DOI:doi: 10.21228/M8JM4K
Project Title:Metabolome Profiling of a Fast-growing Cyanobacterium Synechococcus elongatus PCC 11801 under Diurnal Cycle
Project Type:Measurement of relative metabolite pools under sinusoidal diurnal cycle
Project Summary:The project aims to identify the metabolic changes that occur during diurnal cycle in a fast growing cyanobacterium Synechococcus elongatus PCC 11801. It is a promising host for biofuel production and therefore its studying its metabolism under diurnal condition might provide ideas to engineer it better for growth in outdoor conditions.
Institute:Indian Institute of Technology Bombay
Department:Department of Chemical Engineering
Laboratory:Biosystems Engineering Lab
Last Name:Wangikar
First Name:Pramod P
Address:Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, India - 400076
Email:wangikar@iitb.ac.in
Phone:+91 (22) 2576 7232 (o)
Funding Source:DBT-PAN IIT Centre for Bioenergy (Grant No: BT/EB/PAN IIT/2012)
Contributors:Damini Jaiswal and Pramod P. Wangikar

Subject:

Subject ID:SU001376
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 Time (h) Treatment Condition
SA09429411801 LDC 25-HR BR2 IS IDA-125 MORNING
SA09429511801 LDC 25-HR BR1 IS IDA-325 MORNING
SA09429611801 LDC 25-HR BR1 IS IDA-225 MORNING
SA09429711801 LDC 25-HR BR1 IS IDA-125 MORNING
SA09429811801 LDC 25-HR BR2 IS IDA-225 MORNING
SA09429911801 LDC 25-HR BR3 IS IDA-225 MORNING
SA09430011801 LDC 25-HR BR3 IS IDA-125 MORNING
SA09430111801 LDC 25-HR BR2 IS IDA-325 MORNING
SA09430211801 LDC 25-HR BR3 IS IDA-325 MORNING
SA09430311801 LDC 31-HR BR2 IS IDA-231 MID-DAY
SA09430411801 LDC 31-HR BR1 IS IDA-331 MID-DAY
SA09430511801 LDC 31-HR BR1 IS IDA-231 MID-DAY
SA09430611801 LDC 31-HR BR1 IS IDA-131 MID-DAY
SA09430711801 LDC 31-HR BR2 IS IDA-131 MID-DAY
SA09430811801 LDC 31-HR BR2 IS IDA-331 MID-DAY
SA09430911801 LDC 31-HR BR3 IS IDA-231 MID-DAY
SA09431011801 LDC 31-HR BR3 IS IDA-131 MID-DAY
SA09431111801 LDC 31-HR BR3 IS IDA-331 MID-DAY
SA09431211801 LDC 37-HR BR2 IS IDA-237 EVENING
SA09431311801 LDC 37-HR BR2 IS IDA-337 EVENING
SA09431411801 LDC 37-HR BR3 IS IDA-137 EVENING
SA09431511801 LDC 37-HR BR3 IS IDA-237 EVENING
SA09431611801 LDC 37-HR BR2 IS IDA-137 EVENING
SA09431711801 LDC 37-HR BR1 IS IDA-337 EVENING
SA09431811801 LDC 37-HR BR1 IS IDA-137 EVENING
SA09431911801 LDC 37-HR BR1 IS IDA-237 EVENING
SA09432011801 LDC 37-HR BR3 IS IDA-337 EVENING
SA09432111801 LDC 43-HR BR1 IS IDA-143 MID-NIGHT
SA09432211801 LDC 43-HR BR2 IS IDA-343 MID-NIGHT
SA09432311801 LDC 43-HR BR2 IS IDA-243 MID-NIGHT
SA09432411801 LDC 43-HR BR2 IS IDA-143 MID-NIGHT
SA09432511801 LDC 43-HR BR3 IS IDA-143 MID-NIGHT
SA09432611801 LDC 43-HR BR3 IS IDA-243 MID-NIGHT
SA09432711801 LDC 43-HR BR1 IS IDA-243 MID-NIGHT
SA09432811801 LDC 43-HR BR3 IS IDA-343 MID-NIGHT
SA09432911801 LDC 43-HR BR1 IS IDA-343 MID-NIGHT
SA09428511801 600uE CLDC BR2 IS IDA-2- CONTINUOUS LIGHT ILLUMINATION
SA09428611801 600uE CLDC BR2 IS IDA-1- CONTINUOUS LIGHT ILLUMINATION
SA09428711801 600uE CLDC BR1 IS IDA-3- CONTINUOUS LIGHT ILLUMINATION
SA09428811801 600uE CLDC BR1 IS IDA-1- CONTINUOUS LIGHT ILLUMINATION
SA09428911801 600uE CLDC BR2 IS IDA-3- CONTINUOUS LIGHT ILLUMINATION
SA09429011801 600uE CLDC BR3 IS IDA-2- CONTINUOUS LIGHT ILLUMINATION
SA09429111801 600uE CLDC BR3 IS IDA-1- CONTINUOUS LIGHT ILLUMINATION
SA09429211801 600uE CLDC BR3 IS IDA-3- CONTINUOUS LIGHT ILLUMINATION
SA09429311801 600uE CLDC BR1 IS IDA-2- CONTINUOUS LIGHT ILLUMINATION
Showing results 1 to 45 of 45

Collection:

Collection ID:CO001371
Collection Summary:Experiments were carried out by growing Synechococcus elongatus PCC 11801 cells in multicultivators designed to provide sinusoidal light. The period was 14:10 (light-dark). The samples for metabolomics analysis were collected in the second diurnal cycle at an interval of 6 hours starting from 25th hour (25, 31, 37 and 43 hours). The light intensity amplitude was 600 µmole photons m-2 s-1. Additionally samples were also collected using cells grown under continuous light illumination of 600 µmole photons m-2 s-1 to compare the difference in metabolite levels compared to that in the diurnal cycle. 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

Treatment:

Treatment ID:TR001391
Treatment Summary:The metabolites were extracted using a methanol-chloroform-water method described in the "Sample Collection and Treatment Protocol" file of the collection data.

Sample Preparation:

Sampleprep ID:SP001384
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 AN002168
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:CH001586
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:MS002017
Analysis ID:AN002168
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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