Summary of Study ST000621
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 PR000454. The data can be accessed directly via it's Project DOI: 10.21228/M8CC9H 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 | ST000621 |
| Study Title | Untargeted metabolomic changes in Chlamydomonas reinhardtii treated with lipid inducing small molecules |
| Study Summary | A study to investigate the effect of small molecule lipid inducing compounds that leads to hyper accumulation of lipids in N replete cells of Chlamydomonas reinhardtii. These compounds were identified through a high throughput screening designed for that purpose. During that screening, we screened 43,783 compounds and identified 367 primary hits. These 367 hits were further retested using a 8-point dilution series (from 0.25 to 30 uM) and verified the activity of 250 compounds that induce the hyper lipid accumulating phenotype in algae. Once the hit compounds were identified and confirmed, we then performed extensive chemoinformatics analysis to look for common scaffolds and identified several common substructures. We then selected 15 top performing compounds from 5 diverse structural groups and tested biochemical parameters such as growth, lipid accumulating capacity, effect on photosynthetic rates, respiration rates, oxygen consumption rates, analysis of different lipid species to quantify and identify fatty acid species using GC-MS. To understand the global changes in the metabolome, 2 structurally different compounds were selected and compared with cells grown without compounds as control for untargeted metabolomics analysis. |
| Institute | University of Nebraska-Lincoln |
| Department | Department of Biochemistry |
| Last Name | Wase |
| First Name | Nishikant |
| Address | Department of Biochemistry, 1901 VINE STREET |
| nishikant.wase@gmail.com | |
| Phone | 4023109931 |
| Submit Date | 2017-06-16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-01-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000454 |
| Project DOI: | doi: 10.21228/M8CC9H |
| Project Title: | Untargeted metabolomic changes in Chlamydomonas reinhardtii treated with lipid inducing small molecules |
| Project Summary: | A study to investigate the effect of small molecule lipid inducing compounds that leads to hyper accumulation of lipids in N replete cells of Chlamydomonas reinhardtii. These compounds were identified through a high throughput screening designed for that purpose. During that screening, we screened 43,783 compounds and identified 367 primary hits. These 367 hits were further retested using a 8-point dilution series (from 0.25 to 30 uM) and verified the activity of 250 compounds that induce the hyper lipid accumulating phenotype in algae. Once the hit compounds were identified and confirmed, we then performed extensive chemoinformatics analysis to look for common scaffolds and identified several common substructures. We then selected 15 top performing compounds from 5 diverse structural groups and tested biochemical parameters such as growth, lipid accumulating capacity, effect on photosynthetic rates, respiration rates, oxygen consumption rates, analysis of different lipid species to quantify and identify fatty acid species using GC-MS. To understand the global changes in the metabolome, 2 structurally different compounds were selected and compared with cells grown without compounds as control for untargeted metabolomics analysis. |
| Institute: | University of Nebraska-Lincoln |
| Department: | Biochemistry |
| Laboratory: | FATTTLab |
| Last Name: | Wase |
| First Name: | Nishikant |
| Address: | 1901 Beadle Center, Vine Street, 1901 VINE STREET, Lincoln, NE, 68588-0664, USA |
| Email: | nishikant.wase@gmail.com |
| Phone: | 4023109931 |
| Funding Source: | NCESR-704, Nebraska Center for Energy Science Research; EPS-1004094 and 1264409, National Science Foundation ; NSF CBET : 1402896, National Science Foundation |
| Contributors: | Nishikant Wase, Jiri Adamec, Ron Cerny, Girish Rasineni, Paul N Black, Concetta DiRusso |
Subject:
| Subject ID: | SU000644 |
| Subject Type: | Photosynthetic organism |
| Subject Species: | Chlamydomonas reinhardtii |
| Taxonomy ID: | 3055 |
| Genotype Strain: | CC125 Wild type |
| Species Group: | Microorganism |
Factors:
Subject type: Photosynthetic organism; Subject species: Chlamydomonas reinhardtii (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA035012 | CD06241608 | cmp_030 |
| SA035013 | CD06241609 | cmp_030 |
| SA035014 | CD06241607 | cmp_030 |
| SA035015 | CD06241620 | cmp_784 |
| SA035016 | CD06241619 | cmp_784 |
| SA035017 | CD06241621 | cmp_784 |
| SA035009 | CD06241603 | Control |
| SA035010 | CD06241601B | Control |
| SA035011 | CD06241602 | Control |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO000638 |
| Collection Summary: | Triplicate cultures were grown and treated as indicated and harvested at 72 h. The harvested cells were freeze-dried and weighted 10 ± 0.5 mg dry powder. To extract the metabolites, 500 uL of 75% MeOH in 0.15 M NaCl was added and metabolites were extracted using bead beating 50 Hz for 5 min. The homogenate was sonicated in water bath for 5 min and then 300 uL of 0.15 M NaCl was added and then 1 mL of chloroform:methanol (1:2) with 0.01% BHT was added. Samples were homogenized and allowed to phase separate on ice for 30 mins. Finally tubes were centrifuged for 10 min to separate the polar and non-polar layer. Top polar layer was removed and an aliquot of 200 uL was used for analysis. Samples were evaporated to dryness in SpeedVac and metabolites were reconstituted in 0.03% formic acid in analytical-grade water. Debris was removed via centrifugation and the supernatant was subjected to UPLC-MS analysis. |
| Sample Type: | Photosynthetic organism |
| Collection Method: | Centrifugation from suspension culture. |
| Collection Location: | FATTTLab Department of Biochemistry, Univ of Nebraska-Lincoln |
| Storage Conditions: | After harvest, cells were kept at -80 C until extraction. |
| Collection Vials: | 2 mL Eppendorf tubes |
Treatment:
| Treatment ID: | TR000658 |
| Treatment Summary: | For compound treatment, cells from mid-log phase culture were harvested, washed once with fresh sterile TAP media and inoculated at starting density of 5 x 105 cells/mL. Thus for the current experiment 3 different treatment conditions were generated. Cells without compound treatment were negative control for the lipid accumulation and 2 compounds were used to generate treatment conditions. All compounds were used at a final concentration of 5 M (this concentration was determined using a dose-response curve). For all cultures, 250 mL Erlenmeyer flasks with rubber stopper adopted to facilitate gas exchange were used and maintained in horizontal orbital shaking growing chamber (Innova 43; New Brunswick). At the end of 72h, cells were harvested, media was removed via centrifugation and biomass was stored at -80 C until metabolite extraction. |
| Cell Media: | Tris-Acetate Phoshphate (TAP) media. |
Sample Preparation:
| Sampleprep ID: | SP000651 |
| Sampleprep Summary: | Triplicate cultures were grown and treated as indicated and harvested at 72 h. The harvested cells were freeze-dried and weighted 10 ± 0.5 mg dry powder. To extract the metabolites, 500 uL of 75% MeOH in 0.15 M NaCl was added and metabolites were extracted using bead beating 50 Hz for 5 min. The homogenate was sonicated in water bath for 5 min and then 300 uL of 0.15 M NaCl was added and then 1 mL of chloroform:methanol (1:2) with 0.01% BHT was added. Samples were homogenized and allowed to phase separate on ice for 30 mins. Finally tubes were centrifuged for 10 min to separate the polar and non-polar layer. Top polar layer was removed and an aliquot of 200 uL was used for analysis. Samples were evaporated to dryness in SpeedVac and metabolites were reconstituted in 0.03% formic acid in analytical-grade water. Debris was removed via centrifugation and the supernatant was subjected to UPLC-MS analysis |
| Extraction Method: | Bead beating |
Combined analysis:
| Analysis ID | AN000953 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1200 |
| Column | ACE 5 C18-300 (100 x 2.1mm) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Waters Synapt G2 |
| Ion Mode | POSITIVE |
| Units | intensity |
Chromatography:
| Chromatography ID: | CH000678 |
| Instrument Name: | Agilent 1200 |
| Column Name: | ACE 5 C18-300 (100 x 2.1mm) |
| Flow Rate: | 0.1 mL/min |
| Sample Injection: | 8 uL |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000848 |
| Analysis ID: | AN000953 |
| Instrument Name: | Waters Synapt G2 |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
