Summary of Study ST004392
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 PR002783. The data can be accessed directly via it's Project DOI: 10.21228/M8XK1H This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004392 |
| Study Title | Polar metabolic differences in cortex and hippocampus of wild-type (WT) and Fmr1 KO mice. |
| Study Summary | Fmr1 is a gene that encodes Fragile X mental retardation protein (FMRP). Fmr1-deficient mouse is a knock-out model to study FXS. Fmr1 KO mice, however, do not undergo a CGG expansion or expansion-dependent gene methylation and transcriptional silencing. In addition, some studies indicate that bulk protein synthesis is either unaltered or reduced in the human FXS brain, the opposite of what is observed in Fmr1-deficient mouse brain. Therefore, polar metabolomics were performed to compare cortex and hippocampus between WT and Fmr1 KO mice. There were very few or no polar metabolic changes in mouse Fmr1 KO cortex or hippocampus. |
| Institute | UMass Chan Medical School |
| Last Name | UMass Chan |
| First Name | Spinelli Lab |
| Address | 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA |
| spinellilab@gmail.com | |
| Phone | (508) 856-8989 ext. 68148 |
| Submit Date | 2025-11-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002783 |
| Project DOI: | doi: 10.21228/M8XK1H |
| Project Title: | Metabolic Reprogramming during Human Neuron Differentiation Indicates Glutaminase as a Key Determinant in Fragile X Syndrome |
| Project Summary: | Metabolic homeostasis gone awry is a contributor to, if not an underlying cause of, several neurologic disorders. Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by a trinucleotide repeat expansion in FMR1 and consequent loss of the encoded protein FMRP, which results in downstream molecular, neurologic, and mitochondrial deficits that are linked to cognitive impairment. In human postmortem brain, many metabolites and solute carrier proteins are coordinately dysregulated, which also occurs during differentiation of human iPSCs into excitatory neurons. Metabolic tracing in FXS neurons demonstrates a dearth of glutamine deamidation to glutamate, which reduces anaplerosis into the TCA cycle, potentially hindering bioenergetic and biosynthetic functions of mitochondria. Mechanistically, aberrant expression of glutaminase isoforms in FXS is responsible for reduced glutaminolysis, thereby altering glutamate levels which may contribute to FXS. |
| Institute: | UMass Chan Medical School |
| Last Name: | UMass Chan |
| First Name: | Richter Lab |
| Address: | 55 Lake Avenue North, Worcester, Massachusetts, 01605, USA |
| Email: | spinellilab@gmail.com |
| Phone: | (508) 856-8989 ext. 68148 |
Subject:
| Subject ID: | SU004551 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Male |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA521148 | KO4 ctx | Male Fmr1 KO Mouse Cortex | Fmr1 KO |
| SA521149 | KO3 ctx | Male Fmr1 KO Mouse Cortex | Fmr1 KO |
| SA521150 | KO2 ctx | Male Fmr1 KO Mouse Cortex | Fmr1 KO |
| SA521151 | KO1 ctx | Male Fmr1 KO Mouse Cortex | Fmr1 KO |
| SA521152 | KO1 hpc | Male Fmr1 KO Mouse Hippocampus | Fmr1 KO |
| SA521153 | KO2 hpc | Male Fmr1 KO Mouse Hippocampus | Fmr1 KO |
| SA521154 | KO3 hpc | Male Fmr1 KO Mouse Hippocampus | Fmr1 KO |
| SA521155 | KO4 hpc | Male Fmr1 KO Mouse Hippocampus | Fmr1 KO |
| SA521156 | WT4 ctx | Male WT Mouse Cortex | WT |
| SA521157 | WT1 ctx | Male WT Mouse Cortex | WT |
| SA521158 | WT3 ctx | Male WT Mouse Cortex | WT |
| SA521159 | WT2 ctx | Male WT Mouse Cortex | WT |
| SA521160 | WT2 hpc | Male WT Mouse Hippocampus | WT |
| SA521161 | WT4 hpc | Male WT Mouse Hippocampus | WT |
| SA521162 | WT3 hpc | Male WT Mouse Hippocampus | WT |
| SA521163 | WT1 hpc | Male WT Mouse Hippocampus | WT |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO004544 |
| Collection Summary: | Wild-type and Fmr1 KO mice used were purchased from Jackson laboratories and were housed under a 12 h light/dark cycle with routine monitoring and with free access to food and water. 3-month-old male mice were used in this study (n = 4 each for WT and Fmr1 KO). |
| Sample Type: | Mouse Brain Hippocampus and Cortex |
Treatment:
| Treatment ID: | TR004560 |
| Treatment Summary: | No treatment. |
Sample Preparation:
| Sampleprep ID: | SP004557 |
| Sampleprep Summary: | Tissues were powdered under liquid nitrogen and samples were normalized based on tissue weight. The metabolites were extracted using 80% methanol. The extracts were spun down and the supernatant was vacuum dried before resuspending in LC/MS grade water. |
Combined analysis:
| Analysis ID | AN007339 | AN007340 |
|---|---|---|
| Chromatography ID | CH005568 | CH005568 |
| MS ID | MS007033 | MS007034 |
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH005568 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Merck SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
| Column Temperature: | 25 |
| Flow Gradient: | 20 min, 80% - 20% B; 0.5 min, 20% - 80% B; 7.5min, 80% B |
| Flow Rate: | 0.15ml/min |
| Solvent A: | 100% water; 0.1% ammonium hydroxide; 20mM ammonium carbonate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS007033 |
| Analysis ID: | AN007339 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer was set to full scan (70-1000 m/z), with the spray voltage set to 4.0 kV, heated capillary to 350°C, and the HESI probe at 30 °C. The sheath gas flow was set at 10 units, auxiliary gas at 1 units, and sweep gas flow at 1 unit. The resolution of scan was set to 70,000, AGC target to 1x106, and maximum injection time at 20 msec. Data acquired by Thermo Fisher's Xcalibur software and analyzed by their Tracefinder software. The raw files provided contain data from both positive and negative ion mode. |
| Ion Mode: | POSITIVE |
| MS ID: | MS007034 |
| Analysis ID: | AN007340 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | The mass spectrometer had the spray voltage set to 4.0 kV, heated capillary to 350°C, and the HESI probe at 30 °C. The sheath gas flow was set at 10 units, auxiliary gas at 1 units, and sweep gas flow at 1 unit. An additional scan between 220-700 m/z was used to enhance nucleotide detection in the negative mode as well with the maximum injection time set to 80 msec. Data acquired by Thermo Fisher's Xcalibur software and analyzed by their Tracefinder software. The raw files provided contain data from both positive and negative ion mode. |
| Ion Mode: | NEGATIVE |
