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.
| Study ID | ST001080 |
| Study Title | Dynamic labeling of intracellular metabolites in PCC 7002 |
| Study Type | Timecourse experiment |
| Study 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, 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 |
| Department | Department of Chemical Engineering |
| Laboratory | Bio systems Engineering Lab |
| Last Name | Wangikar |
| First Name | Pramod |
| Address | Powai |
| wangikar@iit.ac.in | |
| Phone | 2225767232 |
| Submit Date | 2018-10-18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-08-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | 32049 |
| 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 |
|---|---|---|
| SA072837 | PCC 7002 180 SEC REP 2 | Wild type |
| SA072838 | PCC 7002 240 SEC REP 1 | Wild type |
| SA072839 | PCC 7002 240 SEC REP 2 | Wild type |
| SA072840 | PCC 7002 180 SEC REP 1 | Wild type |
| SA072841 | PCC 7002 120 SEC REP 2 | Wild type |
| SA072842 | PCC 7002 0 SEC REP 2 | Wild type |
| SA072843 | PCC 7002 60 SEC REP 1 | Wild type |
| SA072844 | PCC 7002 60 SEC REP 2 | Wild type |
| SA072845 | PCC 7002 120 SEC REP 1 | Wild type |
| SA072846 | PCC 7002 0 SEC REP 1 | Wild 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: | 100% water; 15 mM acetic acid; 10 mM tributylamine |
| 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 |
