Summary of Study ST004403
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 | ST004403 |
| Study Title | Polar metabolomics on cell pellets and extracellular media of 4-week iPSC derived forebrain excitatory neurons generated from a FXS and CRISPR edited isogenic control. |
| Study Summary | To assess whether FMRP influences metabolism during neuron maturation, we differentiated isogenic lines into forebrain excitatory neurons and profiled intracellular and extracellular metabolites at weeks 4. Polar metabolites during neuron differentiation revealed that amino acids, energy/nucleotide metabolism, and neurotransmitters were adversely affected in FXS cells and in the culture media at this stage. |
| 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 | 2025-11-13 |
| 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: | SU004562 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Sample type |
|---|---|---|---|---|
| SA521274 | cell FXS_w4_1 | Male Homo sapien iPSCs derived neurons | FXS | Cultured cells |
| SA521275 | cell FXS_w4_2 | Male Homo sapien iPSCs derived neurons | FXS | Cultured cells |
| SA521276 | cell FXS_w4_3 | Male Homo sapien iPSCs derived neurons | FXS | Cultured cells |
| SA521277 | media FXS_w4_1 | Male Homo sapien iPSCs derived neurons | FXS | Extracellular media |
| SA521278 | media FXS_w4_2 | Male Homo sapien iPSCs derived neurons | FXS | Extracellular media |
| SA521279 | media FXS_w4_3 | Male Homo sapien iPSCs derived neurons | FXS | Extracellular media |
| SA521286 | media blank 1 | Male Homo sapien iPSCs derived neurons | media blank | Media Blank |
| SA521280 | cell iControl_w4_1 | Male Homo sapien iPSCs derived neurons | TD | Cultured cells |
| SA521281 | cell iControl_w4_2 | Male Homo sapien iPSCs derived neurons | TD | Cultured cells |
| SA521282 | cell iControl_w4_3 | Male Homo sapien iPSCs derived neurons | TD | Cultured cells |
| SA521283 | media iControl_w4_1 | Male Homo sapien iPSCs derived neurons | TD | Extracellular media |
| SA521284 | media iControl_w4_2 | Male Homo sapien iPSCs derived neurons | TD | Extracellular media |
| SA521285 | media iControl_w4_3 | Male Homo sapien iPSCs derived neurons | TD | Extracellular media |
| Showing results 1 to 13 of 13 |
Collection:
| Collection ID: | CO004555 |
| Collection Summary: | iPSC lines were cultured on Matrigel coated plates in mTeSR™1 (Catalog #85850) with 10uM ROCK inhibitor (Y-27632). Neural induction was performed using the embryoid body formation protocol from StemCell technologies. Briefly cells were plated on Matrigel coated AggreWell™800 wells in STEMdiff™ Neural Induction Medium + SMADi and embryoid bodies were allowed to form for 13 days followed by Rosette selection as per manufactures instructions. The rosettes were plated on Poly-L-Ornithine (PLO)/ laminin coated plates for 3 days and then dissociated into single cells and expanded as NPCs in STEMdiff™ Neural Progenitor Medium. To generate neuron precursors, NPCs were cultured in STEMdiff™ Forebrain Neuron Differentiation media (Catalog #08600) for 3 days on PLO/laminin plates followed by replating at a density of 135,000 cells/cm2 in PLO/laminin plates in STEMdiff™ Forebrain Neuron Maturation media (Catalog #08605) with Compound E for 4 weeks. |
| Sample Type: | Culture Cells and Extracellular Media |
Treatment:
| Treatment ID: | TR004571 |
| Treatment Summary: | No treatment other than standard culturing conditions and genotypes. |
Sample Preparation:
| Sampleprep ID: | SP004568 |
| Sampleprep Summary: | For media, 10ul of sample was added to 90ul of 80% methanol and vortexed for 10mins before spinning to collect the supernatant containing extracted metabolites and vacuum dried. The extract was then resuspended in LC/MS grade water. For extraction from cell pellets from in-vitro cultures, samples were incubated on dry ice with cold 80% methanol. The extracts were spun down and the supernatant was vacuum dried before resuspending in LC/MS grade water. |
Combined analysis:
| Analysis ID | AN007361 | AN007362 |
|---|---|---|
| Chromatography ID | CH005579 | CH005579 |
| MS ID | MS007055 | MS007056 |
| 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 | log2FC(peak area) | log2FC(peak area) |
Chromatography:
| Chromatography ID: | CH005579 |
| 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: | MS007055 |
| Analysis ID: | AN007361 |
| 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: | MS007056 |
| Analysis ID: | AN007362 |
| 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 |
