Summary of Study ST002245
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 PR001433. The data can be accessed directly via it's Project DOI: 10.21228/M8GX29 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.
| Study ID | ST002245 |
| Study Title | Deciphering the metabolomic differences between two fast-growing cyanobacteria, S.elongatus PCC 11801 and 11802 via metabolite profiling |
| Study Summary | The study aims to identify the metabolic differences between two promising fast-growing, non-model cyanobacterial strains, S. elongatus PCC 11801 and PCC 11802. To this end, experiments were carried out to measure metabolite levels in the two cyanobacterial strains grown in shake flasks at a similar light intensity of approx. 300-350 µmole photons.m-2. s-1. The samples for metabolomics analysis were collected during the exponential growth phase at an optical cell density of 0.5-0.6. Isotopic ratio method was utilized to compare the metabolite levels and delineate the differences in their metabolic pathways. |
| Institute | Indian Institute of Technology Bombay |
| Department | Chemical Engineering |
| Last Name | Wangikar |
| First Name | Pramod |
| Address | Biosystems and Bioengineering Lab, Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India -400076 |
| wangikar@iitb.ac.in | |
| Phone | +91 22 2576 72 32 |
| Submit Date | 2022-07-28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-07-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001433 |
| Project DOI: | doi: 10.21228/M8GX29 |
| Project Title: | Comparative Metabolome Profiling of Synechococcus elongatus PCC 11801 and 11802 |
| Project Summary: | The project aims to identify the metabolic differences between two promising non-model cyanobacterial strains, Synechococcus elongatus PCC 11801 and PCC 11802. |
| Institute: | Indian Institute of Technology Bombay |
| Department: | Chemical Engineering |
| Laboratory: | Biosystems and Bioengineering Lab |
| Last Name: | Wangikar |
| First Name: | Pramod |
| Address: | Biosystems and Bioengineering Lab, Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India -400076 |
| Email: | wangikar@iitb.ac.in |
| Phone: | +91 22 2576 72 32 |
| Funding Source: | Department of Biotechnology, Ministry of Science, India |
Subject:
| Subject ID: | SU002331 |
| Subject Type: | Bacteria |
| Subject Species: | Synechococcus elongatus |
| Taxonomy ID: | 2219813 |
Factors:
Subject type: Bacteria; Subject species: Synechococcus elongatus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Strain |
|---|---|---|
| SA214612 | 11801 ES BR3 IS IDA-2 | S.elongatus PCC 11801 |
| SA214613 | 11801 ES BR3 IS IDA-3 | S.elongatus PCC 11801 |
| SA214614 | 11801 ES BR1 IS IDA-1 | S.elongatus PCC 11801 |
| SA214615 | 11801 ES BR2 IS IDA-3 | S.elongatus PCC 11801 |
| SA214616 | 11801 ES BR3 IS IDA-1 | S.elongatus PCC 11801 |
| SA214617 | 11801 ES BR1 IS IDA-2 | S.elongatus PCC 11801 |
| SA214618 | 11801 ES BR2 IS IDA-1 | S.elongatus PCC 11801 |
| SA214619 | 11801 ES BR1 IS IDA-3 | S.elongatus PCC 11801 |
| SA214620 | 11801 ES BR2 IS IDA-2 | S.elongatus PCC 11801 |
| SA214621 | 11802 ES BR3 IS IDA-1 | S.elongatus PCC 11802 |
| SA214622 | 11802 ES BR3 IS IDA-2 | S.elongatus PCC 11802 |
| SA214623 | 11802 ES BR3 IS IDA-3 | S.elongatus PCC 11802 |
| SA214624 | 11802 ES BR2 IS IDA-3 | S.elongatus PCC 11802 |
| SA214625 | 11802 ES BR1 IS IDA-1 | S.elongatus PCC 11802 |
| SA214626 | 11802 ES BR1 IS IDA-2 | S.elongatus PCC 11802 |
| SA214627 | 11802 ES BR1 IS IDA-3 | S.elongatus PCC 11802 |
| SA214628 | 11802 ES BR2 IS IDA-1 | S.elongatus PCC 11802 |
| SA214629 | 11802 ES BR2 IS IDA-2 | S.elongatus PCC 11802 |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO002324 |
| Collection Summary: | Experiments were carried out by growing Synechococcus elongatus PCC 11801 and PCC 11802 cells in shake flask under continuous light conditions. The light intensity was ~300-350 µmole photons m-2 s-1. Twenty mL of culture was collected at OD730 of ~0.5-0.6. 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 the information-dependent acquisition (IDA) method. |
| Sample Type: | Bacterial cells |
Treatment:
| Treatment ID: | TR002343 |
| 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: | SP002337 |
| 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 | AN003665 |
|---|---|
| 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 | Triple TOF |
| MS instrument name | ABI Sciex 5600+ TripleTOF |
| Ion Mode | NEGATIVE |
| Units | Area Ratios |
Chromatography:
| Chromatography ID: | CH002715 |
| 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: | 100% water; 15 mM acetic acid; 10 mM tributylamine |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003416 |
| Analysis ID: | AN003665 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | Triple TOF |
| 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 |
