Summary of Study ST002584
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 PR001664. The data can be accessed directly via it's Project DOI: 10.21228/M8MH79 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002584 |
| Study Title | Metabolomics analysis of ALDH1L1-expressing HuH7 cell lines. |
| Study Summary | One-carbon metabolism is utilized for the de novo synthesis of purines. Given that tumor cells require large amounts of nucleotides, they are highly dependent on one-carbon metabolism. Among the one-carbon-metabolizing enzymes, the aldehyde dehydrogenase 1 family member L1 (ALDH1L1), which catalyzes 10-formyltetrahydrofolate to tetrahydrofolate, is considered a tumor suppressor gene, as its expression is reported to be attenuated or diminished in hepatocellular carcinoma. To clarify the effect of ALDH1L1 expression, we generated control and ALDH1L1-expressing HuH-7 (H7-1L1) cells, and measured the amounts of intracellular metabolites in both control and ALDH1L1-expressing by CE-TOFMS analysis. |
| Institute | Tohoku Medical and Pharmaceutical University |
| Last Name | Sasaki |
| First Name | Masato |
| Address | 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan |
| msasaki@tohoku-mpu.ac.jp | |
| Phone | +81-22-727-0132 |
| Submit Date | 2023-04-21 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-05-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001664 |
| Project DOI: | doi: 10.21228/M8MH79 |
| Project Title: | Metabolomics analysis of ALDH1L1-expressing HuH-7 cell line. |
| Project Summary: | Quantitative metabolomics study of the effect of the folate metabolizing enzyme ALDH1L1 on the HuH-7 cell line. |
| Institute: | Tohoku Medical and Pharmaceutical University |
| Last Name: | Sasaki |
| First Name: | Masato |
| Address: | 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan |
| Email: | msasaki@tohoku-mpu.ac.jp |
| Phone: | +81-22-727-0132 |
Subject:
| Subject ID: | SU002686 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Transgene |
|---|---|---|
| SA259165 | L1-1 | ALDH1L1 |
| SA259166 | L1-3 | ALDH1L1 |
| SA259167 | L1-2 | ALDH1L1 |
| SA259168 | C-3 | empty |
| SA259169 | C-1 | empty |
| SA259170 | C-2 | empty |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO002679 |
| Collection Summary: | ALDH1L1-expressing cells or control (empty vector) cells were cultured in DMEM medium containing 5% fetal bovine serum and metabolites were collected during growing phase. |
| Sample Type: | HuH-7 cells |
Treatment:
| Treatment ID: | TR002698 |
| Treatment Summary: | No treatment in this study. |
Sample Preparation:
| Sampleprep ID: | SP002692 |
| Sampleprep Summary: | Cells were washed with 5%(w/w) mannitol solution, and then extracted with methanol. Extracts were filtered through a 5-kDa cut-off filter (Ultrafree-MC-PLHCC, Human Metabolome Technologies) at 9,100 × g for 2 h at 4 °C, dried in a centrifugal evaporator at 1,500 rpm at 1,000 Pa, and resuspended in 50 μl of ultrapure water before metabolome analysis. |
Combined analysis:
| Analysis ID | AN004255 | AN004256 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | CE | CE |
| Chromatography system | Agilent CE | Agilent CE |
| Column | Agilent Fused silica capillary (80cm x 50um) | Agilent Fused silica capillary (80cm x 50um) |
| MS Type | ESI | ESI |
| MS instrument type | TOF | TOF |
| MS instrument name | Agilent CE-TOFMS | Agilent CE-TOFMS |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Relative Area | relative area |
Chromatography:
| Chromatography ID: | CH003161 |
| Chromatography Summary: | CE-TOFMS (ESI positive) |
| Instrument Name: | Agilent CE |
| Column Name: | Agilent Fused silica capillary (80cm x 50um) |
| Column Temperature: | 20 |
| Flow Gradient: | - |
| Flow Rate: | +30 kV |
| Solvent A: | 1 M formic acid |
| Solvent B: | - |
| Chromatography Type: | CE |
| Chromatography ID: | CH003162 |
| Chromatography Summary: | CE-TOFMS (ESI negative) |
| Instrument Name: | Agilent CE |
| Column Name: | Agilent Fused silica capillary (80cm x 50um) |
| Column Temperature: | 20 |
| Flow Gradient: | - |
| Flow Rate: | −30 kV |
| Solvent A: | 50 mM ammonium acetate |
| Solvent B: | - |
| Chromatography Type: | CE |
MS:
| MS ID: | MS004002 |
| Analysis ID: | AN004255 |
| Instrument Name: | Agilent CE-TOFMS |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using automatic integration software MasterHands (ver.2.16.0.15 Keio University). Signal peaks corresponding to isotopomers, adduct ions, and other product ions of known metabolites were excluded, and remaining peaks were annotated with putative metabolites from the HMT metabolite database based on their migration time and m/z values. Peak areas were normalized to internal standards and sample amounts. |
| Ion Mode: | POSITIVE |
| MS ID: | MS004003 |
| Analysis ID: | AN004256 |
| Instrument Name: | Agilent CE-TOFMS |
| Instrument Type: | TOF |
| MS Type: | ESI |
| MS Comments: | The spectrometer was scanned from m/z 50 to 1,000. Peaks were extracted using automatic integration software MasterHands (ver.2.16.0.15 Keio University). Signal peaks corresponding to isotopomers, adduct ions, and other product ions of known metabolites were excluded, and remaining peaks were annotated with putative metabolites from the HMT metabolite database based on their migration time and m/z values. Peak areas were normalized to internal standards and sample amounts. |
| Ion Mode: | NEGATIVE |
