Summary of Study ST001670
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 PR001073. The data can be accessed directly via it's Project DOI: 10.21228/M80Q4N 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 | ST001670 |
| Study Title | Metabolomics characterization of zebrafish larvae |
| Study Type | MS analysis |
| Study Summary | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. |
| Institute | North Carolina State University |
| Department | Molecular and Structural Biochemistry |
| Last Name | Duan |
| First Name | Likun |
| Address | 120 W Broughton Dr. |
| lduan2@ncsu.edu | |
| Phone | 9195939853 |
| Submit Date | 2021-01-15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-03-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001073 |
| Project DOI: | doi: 10.21228/M80Q4N |
| Project Title: | Reinforcing one-carbon metabolism via folic acid/Folr1 promotes beta-cell formation |
| Project Summary: | Diabetes can be caused by an insufficient beta-cell mass. Here, we performed a genetic screen in a zebrafish model with beta-cell loss to identify pathways promoting beta-cell regeneration. We found that both folate receptor 1 (folr1) overexpression and treatment with folate intermediates, i.e. tetrahydrofolic acid (THF) or folinic acid stimulated beta-cell differentiation in zebrafish. Treatment with these folate intermediates also stimulated beta-cell differentiation in neonatal pig islet cultures, showing the effect could be translated to a mammalian system. In both zebrafish and neonatal pig islets, the increased beta-cell differentiation originated from ductal cells. Mechanistically, comparative metabolomics analyses of zebrafish in the basal state vs following -cell ablation and in un-treated vs folinic acid-treated zebrafish indicated beta-cell regeneration could be attributed to changes in the pyrimidine, carnitine and serine pathways. Overall, our results suggest evolutionary conserved and previously unknown roles of folic acid and one-carbon metabolism in the generation of beta-cell . |
| Institute: | North Carolina State University |
| Department: | Molecular and Structural Biochemistry |
| Last Name: | Duan |
| First Name: | Likun |
| Address: | 120 W Broughton Dr. |
| Email: | lduan2@ncsu.edu |
| Phone: | 9195939853 |
Subject:
| Subject ID: | SU001747 |
| Subject Type: | Fish |
| Subject Species: | Danio rerio |
| Taxonomy ID: | 7955 |
Factors:
Subject type: Fish; Subject species: Danio rerio (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA153395 | CC 02030 metabo reg control 006 | control |
| SA153396 | CC 02030 metabo reg control 005 | control |
| SA153397 | CC 02030 metabo reg control 001 | control |
| SA153398 | AA 02030 metabo control 004 | control |
| SA153399 | AA 02030 metabo control 003 | control |
| SA153400 | AA 02030 metabo control 002 | control |
| SA153401 | AA 02030 metabo control 005 | control |
| SA153402 | AA 02030 metabo control 001 | control |
| SA153403 | CC 02030 metabo reg control 003 | control |
| SA153404 | CC 02030 metabo reg control 002 | control |
| SA153405 | CC 02030 metabo reg control 004 | control |
| SA153385 | BB 02030 metabo FA 004 | Folinic acid |
| SA153386 | BB 02030 metabo FA 005 | Folinic acid |
| SA153387 | DD 02030 metabo reg FA 001 | Folinic acid |
| SA153388 | BB 02030 metabo FA 003 | Folinic acid |
| SA153389 | DD 02030 metabo reg FA 002 | Folinic acid |
| SA153390 | BB 02030 metabo FA 002 | Folinic acid |
| SA153391 | DD 02030 metabo reg FA 005 | Folinic acid |
| SA153392 | DD 02030 metabo reg FA 004 | Folinic acid |
| SA153393 | DD 02030 metabo reg FA 003 | Folinic acid |
| SA153394 | BB 02030 metabo FA 001 | Folinic acid |
| Showing results 1 to 21 of 21 |
Collection:
| Collection ID: | CO001740 |
| Collection Summary: | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Please refer to the publication for more details. |
| Sample Type: | Larvae |
Treatment:
| Treatment ID: | TR001760 |
| Treatment Summary: | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Please refer to the publication for more details. |
Sample Preparation:
| Sampleprep ID: | SP001753 |
| Sampleprep Summary: | Four different treatment groups were used for metabolite characterization: 5 dpf larvae with/without beta-cell ablation and with/without folinic acid treatment. Metabolites were extracted from 5 pooled larvae, and 6 replicates were used per condition. Metabolites were extracted as described previously36. Some of the replicates were used to optimize the analysis of polar metabolites and folate derivatives using Vanquish UHPLC (Thermo Fisher Scientific). Please refer to the publication for more details. |
Combined analysis:
| Analysis ID | AN002725 | AN002726 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | Reversed phase |
| Chromatography system | Vanquish UHPLC (Thermo Fisher Scientific). | Thermo Vanquish UHPLC |
| Column | Waters Xbridge amide HILIC (100 x 2.1mm,3.5um) | Luna C18 LC (150 x 4.6 mm,3um) |
| MS Type | ESI | ESI |
| MS instrument type | Ion trap | Ion trap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | UNSPECIFIED | UNSPECIFIED |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH002011 |
| Chromatography Summary: | For this polar metabolite analysis, a hydrophilic interaction chromatography method (HILIC) with an Xbridge amide column (100 x 2.1 mm i.d., 3.5 µm; Waters) was used for compound separation at 25 °C. Mobile phase A: water with 5 mM ammonium acetate (pH 6.8), and mobile phase B: 100 % acetonitrile. Linear gradient was: 0 min, 85% B; 1.5 min, 85% B; 5.5 min, 35% B; 6.9 min, 35% B; 10.5 min, 35% B; 10.6 min, 10% B; 12.5 min, 10% B; 13.5 min, 85% B; 17.9 min, 85% B; 18 min, 85% B; 20 min, 85% B. The flow rate was: 0-5.5 min, 0.11 ml/min; 6.9-10.5 min, 0.13 ml/min; 10.6-17.9 min, 0.25 ml/min; 18-20 min, 0.11 ml/min. |
| Instrument Name: | Vanquish UHPLC (Thermo Fisher Scientific). |
| Column Name: | Waters Xbridge amide HILIC (100 x 2.1mm,3.5um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 85% B; 1.5 min, 85% B; 5.5 min, 35% B; 6.9 min, 35% B; 10.5 min, 35% B; 10.6 min, 10% B; 12.5 min, 10% B; 13.5 min, 85% B; 17.9 min, 85% B; 18 min, 85% B; 20 min, 85% B. |
| Flow Rate: | 0-5.5 min, 0.11 ml/min; 6.9-10.5 min, 0.13 ml/min; 10.6-17.9 min, 0.25 ml/min; 18-20 min, 0.11 ml/min |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 6.8 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH002012 |
| Chromatography Summary: | The analysis of folic acid and its derivatives was performed using Luna column (100 x 3 mm i.d., 3 µm, C18(2), 100 Å, Phenomenex) at 25 °C. Mobile phase A: water with 0.1% formic acid, and mobile phase B: 100 % methanol. Linear gradient was: 0 min, 2% B; 1.5 min, 2% B; 3.0 min, 15% B; 5.5 min, 95% B; 14.5 min, 95% B; 15.0 min, 2% B; 22.0 min, 2% B. The flow rate was 0.150 ml/min. |
| Chromatography Comments: | Luna® 3 µm C18(2) 100 Å, LC Column 150 x 4.6 mm, Ea |
| Instrument Name: | Thermo Vanquish UHPLC |
| Column Name: | Luna C18 LC (150 x 4.6 mm,3um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 2% B; 1.5 min, 2% B; 3.0 min, 15% B; 5.5 min, 95% B; 14.5 min, 95% B; 15.0 min, 2% B; 22.0 min, 2% B. |
| Flow Rate: | 0.150 ml/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002522 |
| Analysis ID: | AN002725 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | Xcalibur 4.4 from Thermo Scientific for data acquisition and we use Sieve 2.2 for chromatographic alignment and peak integration.To analyze polar metabolites, the mass spectrometer was equipped with a HESI probe and operated in the positive/negative switching mode. The relevant parameters were as listed: vaporizer temperature, 350 °C; ion transfer tube temperature, 300 °C; sheath gas, 35; auxiliary gas, 7; sweep gas, 1; spray voltage, 3.5 kV for positive mode and 2.5 kV for negative mode; RF-lens (%), 30. The resolution was set at 60,000 (at m/z 200). Automatic maximum injection time (max IT) and automated gain control (AGC) were used. |
| Ion Mode: | UNSPECIFIED |
| MS ID: | MS002523 |
| Analysis ID: | AN002726 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | Xcalibur 4.4 from Thermo Scientific for data acquisition and we use Sieve 2.2 for chromatographic alignment and peak integration.To measure folate derivatives, Orbitrap Exploris 480 was operated in SIM mode (selected ion monitoring) targeting the following ions: folic acid (442.1470), 5-methyltetrahydrofolate (460.1939), and folinic acid (474.1732). |
| Ion Mode: | UNSPECIFIED |
