Summary of Study ST003019
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 PR001759. The data can be accessed directly via it's Project DOI: 10.21228/M8BH9K 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 | ST003019 |
Study Title | Metabolomic profiling of PMM2-CDG brain organoids by GC/MS |
Study Summary | PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the PMM enzyme, which leads to impaired protein glycosylation. While the disorder has primarily neurological presentation, there is limited knowledge about the specific brain-related changes that result from PMM deficiency. Utilizing 3D brain organoids derived from individuals with PMM2-CDG, we identified abnormal glucose metabolism in PMM2-CDG organoids, indicating disturbances in metabolic utilization. In this experiment, day 160 organoids were used. |
Institute | Mayo Clinic |
Last Name | Radenkovic |
First Name | Silvia |
Address | 200 2nd Ave SW Rochester MN, USA |
radenkovic.silvia@mayo.edu | |
Phone | 507(77) 6-6107 |
Submit Date | 2023-12-19 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzML |
Analysis Type Detail | GC-MS |
Release Date | 2024-12-20 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001759 |
Project DOI: | doi: 10.21228/M8BH9K |
Project Title: | Metabolomic profiling of PMM2-CDG brain organoids |
Project Summary: | PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the PMM enzyme, which leads to impaired protein glycosylation. While the disorder has primarily neurological presentation, there is limited knowledge about the specific brain-related changes that result from PMM deficiency. Utilizing 3D brain organoids derived from individuals with PMM2-CDG, we identified abnormal glucose metabolism in PMM2-CDG organoids, indicating disturbances in metabolic utilization. |
Institute: | Mayo Clinic |
Last Name: | Radenkovic |
First Name: | Silvia |
Address: | 200 2nd Ave SW Rochester MN |
Email: | radenkovic.silvia@mayo.edu |
Phone: | 507(77) 6-6107 |
Funding Source: | NIH, KU Leuven |
Subject:
Subject ID: | SU003133 |
Subject Type: | Mammal |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Genotype Strain: | WT/PMM2-CDG |
Age Or Age Range: | 5-25 |
Gender: | Male and female |
Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Homo sapiens (Factor headings shown in green)
mb_sample_id | local_sample_id | Genotype |
---|---|---|
SA327663 | S5 | CTR |
SA327664 | S1 | CTR |
SA327665 | S3 | CTR |
SA327666 | S6 | PMM2 |
SA327667 | S4 | PMM2 |
SA327668 | S2 | PMM2 |
Showing results 1 to 6 of 6 |
Collection:
Collection ID: | CO003126 |
Collection Summary: | Brain were collected at day in vitro 160. Briefly, 5 organoids per cell line were collected and washed three times in DPBS (Gibco). The DPBS was then removed, the organoids flash frozen and kept in -80 °C prior to metabolomics experiments. The metabolites were extracted using two phase extraction protocol. First, the organoids were transferred to lysing matrix tube and 350 µL of ice-cold extraction buffer (80 % MeOH, IS) was added to the sample. Next, the organoids were lyzed with ribolyzer, the lysate transferred to 1.5 mL Eppendorf tube and placed overnight at -80 °C. Further, the samples were centrifuged at 15,000 rpm, 4 °C, 20 min. 100 µL of supernatant was transferred to a fresh Eppendorf tube and 35 µL of ddH20 was added, followed by 800 µL 100% chloroform. The samples were then vortexed and stored at 4 °C overnight. Next, the polar phase was the used for Gas Chromatography/Mass Spectrometry (GC/MS) |
Sample Type: | Brain organoids |
Storage Conditions: | -80℃ |
Treatment:
Treatment ID: | TR003142 |
Treatment Summary: | Samples were not treated |
Sample Preparation:
Sampleprep ID: | SP003139 |
Sampleprep Summary: | The metabolites were extracted from the brain organoids using double phase metabolite extration. Standards containing metabolites of interest were prepared simultaneously and dried overnight together with cellular extracts by vacuum centrifugation at 4 °C. The following day, 20 µL of methoxyamine (MOX) (Sigma Aldrich) was added to the samples and they were incubated for 90 min at 37 °C. Next, 60 µL of N, O-bis(trimethylsilyl)trifluoroacetamide (TMS) (Sigma Aldrich) was added to the samples, which were then incubated at 60 °C for 30 min. Samples were kept overnight in a dry and cool place to allow further derivatization with TMS |
Processing Storage Conditions: | -80℃ |
Extract Storage: | -80℃ |
Sample Derivatization: | MOX, TMS |
Combined analysis:
Analysis ID | AN004953 |
---|---|
Analysis type | MS |
Chromatography type | GC |
Chromatography system | Agilent 7890A |
Column | Agilent HP-5ms (30m x 0.25mm, 0.25um) |
MS Type | EI |
MS instrument type | Triple quadrupole |
MS instrument name | Agilent 7000B |
Ion Mode | POSITIVE |
Units | AUC |
Chromatography:
Chromatography ID: | CH003737 |
Chromatography Summary: | Agilent 7890A GC (Agilent Technologies) coupled with an HP-5 ms 5 % phenyl methyl silox capillary column (30 m, 0.25 mm, 0.25 um, Agilent Technologies). The temperature gradient applied was as follows: 2 min 100°C, next 175 °C at Δ20 °C/min, followed by an increase to 230 °C at Δ4 °C/min, kept at 230 °C for 3 min, increased to 300 °C at Δ 40°C/min and lastly kept at 300 °C for 5 min. The column was further baked for another 3 min at 325 °C after the gradient. |
Instrument Name: | Agilent 7890A |
Column Name: | Agilent HP-5ms (30m x 0.25mm, 0.25um) |
Column Temperature: | Gradient |
Flow Gradient: | N/A |
Flow Rate: | NA |
Solvent A: | N/A |
Solvent B: | N/A |
Chromatography Type: | GC |
MS:
MS ID: | MS004693 |
Analysis ID: | AN004953 |
Instrument Name: | Agilent 7000B |
Instrument Type: | Triple quadrupole |
MS Type: | EI |
MS Comments: | Mass Hunter Workstation software with the Quantitative Analysis Version B.06.00/Build 6.0.388.0 and el-maven polly software. Specific metabolites were identified based on their fragment formula/elution time |
Ion Mode: | POSITIVE |