Summary of Study ST002281
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 PR001461. The data can be accessed directly via it's Project DOI: 10.21228/M8W122 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 | ST002281 |
| Study Title | Metabolite patterns between isogenic normal hiPSCs and Trisomy hiPSC |
| Study Summary | We wanted to compare metabolites patterns between isogenic normal hiPSCs and Trisomy hiPSCs. All hiPSCs cell lines were generated from same mosaic Down symdrome patient. |
| Institute | Guangdong Provincial People's Hospital |
| Department | Medical Research Center |
| Laboratory | Liu lab |
| Last Name | Liu |
| First Name | Juli |
| Address | Zhongshan 2nd road |
| liujuli@gdph.org.cn | |
| Phone | +8602083827812 |
| Submit Date | 2022-09-09 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | APCI-MS |
| Release Date | 2024-09-13 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001461 |
| Project DOI: | doi: 10.21228/M8W122 |
| Project Title: | Metabolite patterns between isogenic normal hiPSCs and Trisomy hiPSCs |
| Project Summary: | We wanted to compare metabolites patterns between isogenic normal hiPSCs and Trisomy hiPSCs. All hiPSCs cell lines were generated from same mosaic Down symdrome patient. |
| Institute: | Guangdong provincial people's hospital |
| Department: | Medical Research Center |
| Laboratory: | Liu Lab |
| Last Name: | Liu |
| First Name: | Juli |
| Address: | Zhongshan 2nd road |
| Email: | liujuli@gdph.org.cn |
| Phone: | +8602083827812 |
Subject:
| Subject ID: | SU002367 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Cell Strain Details: | Human pluripotent stem cells |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Treatment |
|---|---|---|---|
| SA218473 | HFX3_1074585_CN_blank | blank | negative mode-blank |
| SA218474 | HFX3_1074585_CP_blank | blank | positive mode-blank |
| SA218475 | HFX3_CN1_FZTM220002975-1A_N1 group | isogenic normal hiPSCs (N1) | negative mode-normal |
| SA218476 | HFX3_CP1_FZTM220002975-1A_N1 group | isogenic normal hiPSCs (N1) | positive mode-normal |
| SA218477 | HFX3_CN2_FZTM220002976-1A_N2 group | isogenic normal hiPSCs (N2) | negative mode-normal |
| SA218478 | HFX3_CP2_FZTM220002976-1A_N2 group | isogenic normal hiPSCs (N2) | positive mode-normal |
| SA218479 | HFX3_CN3_FZTM220002977-1A_N3 group | isogenic normal hiPSCs (N3) | negative mode-normal |
| SA218480 | HFX3_CP3_FZTM220002977-1A_N3 group | isogenic normal hiPSCs (N3) | positive mode-normal |
| SA218481 | HFX3_1074585_CN_QC1 | quality control 1 (QC1) | negative mode-quality control 1 (QC1) |
| SA218482 | HFX3_1074585_CP_QC1 | quality control 1 (QC1) | positive mode-quality control 1 (QC1) |
| SA218483 | HFX3_1074585_CN_QC2 | quality control 2 (QC2) | negative mode-quality control 2 (QC2) |
| SA218484 | HFX3_1074585_CP_QC2 | quality control 2 (QC2) | positive mode-quality control 2 (QC2) |
| SA218485 | HFX3_1074585_CN_QC3 | quality control 3 (QC3) | negative mode-quality control 3 (QC3) |
| SA218486 | HFX3_1074585_CP_QC3 | quality control 3 (QC3) | positive mode-quality control 3 (QC3) |
| SA218467 | HFX3_CN4_FZTM220002978-1A_P1 group | Trisomy 21 hiPSCs (P1) | negative mode-Trisomy 21 |
| SA218468 | HFX3_CP4_FZTM220002978-1A_P1 group | Trisomy 21 hiPSCs (P1) | positive mode-Trisomy 21 |
| SA218469 | HFX3_CN5_FZTM220002979-1A_P2 group | Trisomy 21 hiPSCs (P2) | negative mode-Trisomy 21 |
| SA218470 | HFX3_CP5_FZTM220002979-1A_P2 group | Trisomy 21 hiPSCs (P2) | positive mode-Trisomy 21 |
| SA218471 | HFX3_CN6_FZTM220002980-1A_P3 group | Trisomy 21 hiPSCs (P3) | negative mode-Trisomy 21 |
| SA218472 | HFX3_CP6_FZTM220002980-1A_P3 group | Trisomy 21 hiPSCs (P3) | positive mode-Trisomy 21 |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO002360 |
| Collection Summary: | Metabolites patterns between isogenic hiPSCs and Trisomy 21 hiPSCs. |
| Sample Type: | iPSC cells |
| Storage Conditions: | Room temperature |
Treatment:
| Treatment ID: | TR002379 |
| Treatment Summary: | All hiPSCs were cultured in mTesR1 medium in 6-well plate pre-coated with Matrigel in 37 degree. |
Sample Preparation:
| Sampleprep ID: | SP002373 |
| Sampleprep Summary: | The samples were placed in the EP tubes and resuspended with prechilled 80% methanol by well vortex. Then the samples were melted on ice and whirled for 30 s. After the sonification for 6 min, they were centrifuged at 5,000 rpm, 4°C for 1 min. The supernatant was freeze-dried and dissolvedwith 10% methanol. Finally, the solution was injected into the LC-MS/MS system analysis. |
Combined analysis:
| Analysis ID | AN003725 | AN003726 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Hypesil Gold | Hypesil Gold |
| MS Type | APCI | APCI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF-X Orbitrap | Thermo Q Exactive HF-X Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | pmoles/l | pmoles/l |
Chromatography:
| Chromatography ID: | CH002759 |
| Chromatography Summary: | UHPLC-MS/MS analyses were performed using a Vanquish UHPLC system (ThermoFisher, Germany) coupled with an Orbitrap Q ExactiveTMHF-X mass spectrometer (Thermo Fisher,Germany) in Novogene Co., Ltd. (Beijing, China). Samples were injected onto a Hypesil Gold column (100×2.1 mm, 1.9µm) using a 17-min linear gradient at a flow rate of 0.2mL/min. The eluents for the positive polarity mode were eluent A (0.1% FA in Water) and eluent B (Methanol).The eluents for the negative polarity mode were eluent A (5 mMammonium acetate, pH 9.0) and eluent B (Methanol).The solvent gradient was set as follows: 2% B, 1.5 min; 2-100% B, 3 min; 100% B, 10 min;100-2% B, 10.1 min;2% B, 12 min. Q ExactiveTM HF-X mass spectrometer was operated in positive/negative polarity mode with spray voltage of 3.5 kV, capillary temperature of 320°C, sheath gas flow rate of 35 psi and aux gas flow rate of 10 L/min, S-lens RF level of 60, Aux gas heater temperature of 350°C. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Hypesil Gold |
| Flow Gradient: | 2% B, 1.5 min; 2-100% B, 3 min; 100% B, 10 min;100-2% B, 10.1 min;2% B, 12 min |
| Flow Rate: | 0.2mL/min |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 9.0 |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003473 |
| Analysis ID: | AN003725 |
| Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | APCI |
| MS Comments: | The raw data files generated by UHPLC-MS/MS were processed using the Compound Discoverer 3.1 (CD3.1, ThermoFisher) to perform peak alignment, peak picking, and quantitation for each metabolite. The main parameters were set as follows: retention time tolerance, 0.2 minutes; actual mass tolerance, 5ppm; signal intensity tolerance, 30%; signal/noise ratio, 3; and minimum intensity, et al. After that, peak intensities were normalized to the total spectral intensity.The normalized data was used to predict the molecular formula based on additive ions, molecular ion peaks and fragment ions. And then peaks were matched with the mzCloud (https://www.mzcloud.org/),mzVault and MassList database to obtain the accurate. qualitative and relative quantitative results. |
| Ion Mode: | POSITIVE |
| MS ID: | MS003474 |
| Analysis ID: | AN003726 |
| Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | APCI |
| MS Comments: | The raw data files generated by UHPLC-MS/MS were processed using the Compound Discoverer 3.1 (CD3.1, ThermoFisher) to perform peak alignment, peak picking, and quantitation for each metabolite. The main parameters were set as follows: retention time tolerance, 0.2 minutes; actual mass tolerance, 5ppm; signal intensity tolerance, 30%; signal/noise ratio, 3; and minimum intensity, et al. After that, peak intensities were normalized to the total spectral intensity.The normalized data was used to predict the molecular formula based on additive ions, molecular ion peaks and fragment ions. And then peaks were matched with the mzCloud (https://www.mzcloud.org/),mzVault and MassList database to obtain the accurate. qualitative and relative quantitative results. |
| Ion Mode: | NEGATIVE |
