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.

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Study IDST002584
Study TitleMetabolomics analysis of ALDH1L1-expressing HuH7 cell lines.
Study SummaryOne-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 NameSasaki
First NameMasato
Address4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi, 981-8558, Japan
Emailmsasaki@tohoku-mpu.ac.jp
Phone+81-22-727-0132
Submit Date2023-04-21
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-05-01
Release Version1
Masato Sasaki Masato Sasaki
https://dx.doi.org/10.21228/M8MH79
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Transgene
SA259165L1-1ALDH1L1
SA259166L1-3ALDH1L1
SA259167L1-2ALDH1L1
SA259168C-3empty
SA259169C-1empty
SA259170C-2empty
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 Other Other
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:Other
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:Other
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
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