Summary of Study ST002743
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 PR001708. The data can be accessed directly via it's Project DOI: 10.21228/M8XM8H This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002743 |
| Study Title | Metabolomics comparison of lung fibroblasts from Pteropus alecto and Homo sapiens |
| Study Type | MS Quantitative analysis |
| Study Summary | Targeted Metabolomics was performed to identify differences in central carbon metabolism between lung fibroblasts from black flying fox fruit bat Pteropus alecto (PaLung cells) and Humans (WI-38 cells). For both PaLung and WI-38 cells, metabolomics measurements were carried out for n = 3 biological replicates. |
| Institute | Duke-NUS Medical School |
| Last Name | Jagannathan |
| First Name | Narendra Suhas |
| Address | 8 College Road, Singapore, Singapore, 169857, Singapore |
| gmsnsja@nus.edu.sg | |
| Phone | (65) 66015073 |
| Submit Date | 2023-06-25 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-06-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001708 |
| Project DOI: | doi: 10.21228/M8XM8H |
| Project Title: | Metabolomics comparison of lung fibroblasts from Pteropus alecto and Homo sapiens |
| Project Type: | MS quantitative analysis |
| Project Summary: | Targeted Metabolomics was performed to identify differences in central carbon metabolism between lung fibroblasts from black flying fox fruit bat Pteropus alecto (PaLung cells) and Humans (WI-38 cells). |
| Institute: | Duke-NUS Medical School |
| Last Name: | Jagannathan |
| First Name: | Narendra Suhas |
| Address: | Centre for Computational Biology, 8 College Road, Singapore, Singapore, 169857, Singapore |
| Email: | gmsnsja@nus.edu.sg |
| Phone: | (65) 66015073 |
| Project Comments: | Metabolomics was performed by commissioning to Human Metabolome Technologies (HMT) service. |
| Contributors: | Javier Yu Peng Koh, Yoko Itahana, Koji Itahana, Lisa Tucker-Kellogg |
Subject:
| Subject ID: | SU002850 |
| Subject Type: | Cultured cells |
| Subject Species: | Pteropus alecto / Homo sapiens |
Factors:
Subject type: Cultured cells; Subject species: Pteropus alecto / Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Species |
|---|---|---|---|
| SA289154 | WI38-1 | Wild-type | H. sapiens |
| SA289155 | WI38-3 | Wild-type | H. sapiens |
| SA289156 | WI38-2 | Wild-type | H. sapiens |
| SA289157 | PaLung-3 | Wild-type | P. alecto |
| SA289158 | PaLung-1 | Wild-type | P. alecto |
| SA289159 | PaLung-2 | Wild-type | P. alecto |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO002843 |
| Collection Summary: | WI-38 and PaLung cells were seeded in a 100 mm dish and harvested 2 days after seeding according to the protocol provided by Human Metabolome Technologies (HMT Japan). |
| Sample Type: | Cultured fibroblasts |
Treatment:
| Treatment ID: | TR002859 |
| Treatment Summary: | PaLung and WI-38 cells were washed with 5% (w/w) mannitol twice and fixed with methanol containing the internal standard solution. The internal standard solution was provided by HMT. Lysates were centrifuged at 2,300 x g for 5 min at 4°C, and supernatants were filtered using the provided filter units by centrifuging at 9,100 × g for 3 hours at 4 °C. Filtrates were evaporated by SpeedVac Concentrator SPD1010 (Thermo Fisher Scientific) and submitted to HMT for analysis. The total cell numbers at the time of harvest were about 1.4 x 107 cells for each cell line. Targeted quantitative analysis was performed by HMT using capillary electrophoresis mass spectrometry (CE-TOFMS and CE-QqQMS). Absolute abundances (normalized by cell numbers) were obtained for a total of 116 metabolites (54 and 62 metabolites in the cation and anion modes, respectively). |
Sample Preparation:
| Sampleprep ID: | SP002856 |
| Sampleprep Summary: | PaLung and WI-38 cells were washed with 5% (w/w) mannitol twice and fixed with methanol containing the internal standard solution. The internal standard solution was provided by HMT. Lysates were centrifuged at 2,300 x g for 5 min at 4°C, and supernatants were filtered using the provided filter units by centrifuging at 9,100 × g for 3 hours at 4 °C. Filtrates were evaporated by SpeedVac Concentrator SPD1010 (Thermo Fisher Scientific) and submitted to HMT for analysis. The total cell numbers at the time of harvest were about 1.4 x 107 cells for each cell line. Targeted quantitative analysis was performed by HMT using capillary electrophoresis mass spectrometry (CE-TOFMS and CE-QqQMS). Absolute abundances (normalized by cell numbers) were obtained for a total of 116 metabolites (54 and 62 metabolites in the cation and anion modes, respectively). |
Combined analysis:
| Analysis ID | AN004447 | AN004448 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | CE | CE |
| Chromatography system | Agilent CE | Agilent CE |
| Column | Fused silica capillary, i.d. 50 μm × 80 cm | Fused silica capillary, i.d. 50 μm × 80 cm |
| MS Type | ESI | ESI |
| MS instrument type | Other | Triple quadrupole |
| MS instrument name | Agilent CE-TOFMS | Agilent 6460 QQQ |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | pmol/10^6 cells | pmol/10^6 cells |
Chromatography:
| Chromatography ID: | CH003341 |
| Instrument Name: | Agilent CE |
| Column Name: | Fused silica capillary, i.d. 50 μm × 80 cm |
| Column Temperature: | NA |
| Flow Gradient: | NA |
| Flow Rate: | NA |
| Solvent A: | NA |
| Solvent B: | NA |
| Chromatography Type: | CE |
MS:
| MS ID: | MS004194 |
| Analysis ID: | AN004447 |
| Instrument Name: | Agilent CE-TOFMS |
| Instrument Type: | Other |
| MS Type: | ESI |
| MS Comments: | Peaks detected in CE-TOFMS analysis were extracted using automatic integration software (MasterHands ver.2.18.0.1 developed at Keio University) (4) and those in CE-QqQMS analysis were extracted using automatic integration software (MassHunter Quantitative Analysis B.06.00 Agilent Technologies, Santa Clara, CA, USA) in order to obtain peak information, which includes m/z, migration time (MT), and peak area. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004195 |
| Analysis ID: | AN004448 |
| Instrument Name: | Agilent 6460 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Peaks detected in CE-TOFMS analysis were extracted using automatic integration software (MasterHands ver.2.18.0.1 developed at Keio University) (4) and those in CE-QqQMS analysis were extracted using automatic integration software (MassHunter Quantitative Analysis B.06.00 Agilent Technologies, Santa Clara, CA, USA) in order to obtain peak information, which includes m/z, migration time (MT), and peak area. |
| Ion Mode: | NEGATIVE |
