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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001180 |
| Study Title | Metabolome Profiling of Synechococcus elogatus PCC 11802 |
| Study Type | Quantitative Metabolomics |
| Study 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 P |
| Address | Powai |
| wangikar@iitb.ac.in | |
| Phone | +91 (22) 2576 7232 |
| Submit Date | 2019-05-07 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-05-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | 2283154 |
Factors:
Subject type: Bacteria; Subject species: Synechococcus elongatus PCC 11802 (Factor headings shown in green)
| mb_sample_id | local_sample_id | Conditions |
|---|---|---|
| SA081616 | PCC 11802 1 PERCENT CO2 R3 | 1% CO2 |
| SA081617 | PCC 11802 1 PERCENT CO2 R2 | 1% CO2 |
| SA081618 | PCC 11802 1 PERCENT CO2 R1 | 1% CO2 |
| SA081619 | PCC 11802 AMBIENT CO2 R2 | Ambient CO2 |
| SA081620 | PCC 11802 AMBIENT CO2 R3 | Ambient CO2 |
| SA081621 | PCC 11802 AMBIENT CO2 R1 | Ambient 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 | Triple TOF |
| 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: | 100% water; 15 mM acetic acid; 10 mM tributylamine |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001813 |
| Analysis ID: | AN001958 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | Triple TOF |
| 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 |
