Summary of Study ST001290
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 PR000872. The data can be accessed directly via it's Project DOI: 10.21228/M8ZT30 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 | ST001290 |
| Study Title | Lipidome Signatures of Metastasis in a Transgenic Mouse Model of Sonic Hedgehog Medulloblastoma. |
| Study Type | Untargeted metabolomics |
| Study Summary | Metabolic alternations were investigated by applying Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) to mice brain tissue samples collected from SmoA1-Math-GFP mice with (n=18) and without (n=7) metastasis. All samples were analyzed using reverse phase (RP) UPLC-MS analysis in positive and negative ion modes. |
| Institute | Georgia Institute of Technology |
| Department | Chemistry |
| Laboratory | Fernández |
| Last Name | Huang |
| First Name | Danning |
| Address | 901 Atlantic Dr NE |
| dhuang74@gatech.edu | |
| Phone | 4045127523 |
| Submit Date | 2019-12-13 |
| Num Groups | 2 |
| Total Subjects | 25 |
| Num Males | 5 |
| Num Females | 20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-12-16 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000872 |
| Project DOI: | doi: 10.21228/M8ZT30 |
| Project Title: | Lipidome Signatures of Metastasis in a Transgenic Mouse Model of Sonic Hedgehog Medulloblastoma. |
| Project Type: | Untargeted metabolomics |
| Project Summary: | Medulloblastoma (MB), the most common malignant pediatric brain tumor, has high propensity to metastasize. Currently, the standard treatment for MB patients includes radiation therapy administered to the entire brain and spine for the purpose of treating or preventing against metastasis. Due to this aggressive treatment, the majority of long-term survivors will be left with permanent and debilitating neurocognitive impairments and, for the 30-40% patients that fail to respond to radiation, all will relapse with terminal metastatic disease. An understanding of the underlying biology that drives MB metastasis is lacking, and is critically needed in order to develop targeted therapeutics for its prevention. To examine the metastatic biology of sonic hedgehog (SHH) MB, the human MB subgroup with the worst clinical outcome, we first generated a robust SmoA1-Math-GFP mouse model that reliably reproduces human SHH MB whereby metastases can be visualized under fluorescence microscopy. Lipidome alterations associated with metastasis were then investigated by applying Ultra-Performance Liquid Chromatography Mass Spectrometry (UPLC-MS) under both positive and negative ionization modes to primary tumor samples collected from mice with (n=18) and without (n=7) metastasis. This study provides the first insights into dysregulations of lipid metabolism associated with SHH MB metastatic progression, and thus serves as a guide toward novel targeted therapies. |
| Institute: | Georgia Institute of Technology |
| Department: | Chemistry |
| Laboratory: | Fernández |
| Last Name: | Huang |
| First Name: | Danning |
| Address: | 901 Atlantic Dr NE, Atlanta, GA, 30332, USA |
| Email: | dhuang74@gatech.edu |
| Phone: | 404-512-7523 |
Subject:
| Subject ID: | SU001362 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | SmoA1-Math-GFP |
| Age Or Age Range: | 12-36 weeks |
| Gender: | Male and female |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Mice strain | Group |
|---|---|---|---|
| SA093716 | SGTA3 | SmoA1-Math-GFP | PT |
| SA093717 | SG215 | SmoA1-Math-GFP | PT |
| SA093718 | SGTA10 | SmoA1-Math-GFP | PT |
| SA093719 | SG105 | SmoA1-Math-GFP | PT |
| SA093720 | SG138 | SmoA1-Math-GFP | PT |
| SA093721 | CASE40 | SmoA1-Math-GFP | PT |
| SA093722 | SG113 | SmoA1-Math-GFP | PT |
| SA093723 | SGTA9 | SmoA1-Math-GFP | PT |
| SA093724 | SGTA4 | SmoA1-Math-GFP | PT |
| SA093725 | SG221 | SmoA1-Math-GFP | PT |
| SA093726 | SGTA11 | SmoA1-Math-GFP | PT |
| SA093727 | SG218 | SmoA1-Math-GFP | PT |
| SA093728 | SG223 | SmoA1-Math-GFP | PT |
| SA093729 | SG174 | SmoA1-Math-GFP | PT |
| SA093730 | SG203 | SmoA1-Math-GFP | PT |
| SA093731 | SG204 | SmoA1-Math-GFP | PT |
| SA093732 | SG217 | SmoA1-Math-GFP | PT |
| SA093733 | SG175 | SmoA1-Math-GFP | PT |
| SA093734 | CASE41 | SmoA1-Math-GFP | PTMT |
| SA093735 | SG222 | SmoA1-Math-GFP | PTMT |
| SA093736 | SG191 | SmoA1-Math-GFP | PTMT |
| SA093737 | SGTA12 | SmoA1-Math-GFP | PTMT |
| SA093738 | SGTA13 | SmoA1-Math-GFP | PTMT |
| SA093739 | SG228 | SmoA1-Math-GFP | PTMT |
| SA093740 | SGTA | SmoA1-Math-GFP | PTMT |
| Showing results 1 to 25 of 25 |
Collection:
| Collection ID: | CO001356 |
| Collection Summary: | Mice brain and spinal cord were dissected from each mouse and fluorescence microscopy was used to visualize the tumors. Mice having a GFP signal in the cerebellum only were designated as having a primary tumor without metastasis (PT group, n=18). Mice having a strong GFP signal in the cerebellum and positive GFP signal in the spinal cord were designated as having a primary tumor with metastasis (PTMT group, n=7). With aid of GFP visualization, the primary tumor in each mouse brain was cut from the cerebellum, and immediately frozen using liquid nitrogen, and stored at -80 °C. |
| Sample Type: | Brain |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001377 |
| Treatment Summary: | SmoA1-Math1-GFP mice were generated by crossing SmoA1 mice with Math1-driven GFP reporter mice. All mice were kept under the same condition and typically developed detectable MB tumors by MR imaging and clinical symptoms around 23 weeks. |
Sample Preparation:
| Sampleprep ID: | SP001370 |
| Sampleprep Summary: | Frozen mice brain tissue samples were cryo-pulverized with liquid nitrogen and weighed. 2-propanol (20 uL/mg) was added to the cryo-pulverized tissue samples to precipitate proteins. Samples were vortex-mixed for 1 min, and centrifuged at 13,000 rpm for 7 min. Following centrifugation, 100 uL of supernatant was transferred to an autosampler vial and analyzed with UPLC-MS. A blank sample, prepared with 100 uL 2-propanol, underwent the same process as the murine tumor samples. A pooled quality control (QC) sample was prepared by mixing a 10 uL aliquot of supernatant of each sample. |
Combined analysis:
| Analysis ID | AN002143 | AN002144 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Normalized Peak Abundance | Normalized Peak Abundance |
Chromatography:
| Chromatography ID: | CH001569 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Waters Acquity BEH C18 (50 x 2.1mm,1.7um) |
| Column Temperature: | 55 |
| Sample Injection: | 5μL |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001995 |
| Analysis ID: | AN002143 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed in positive and negative ion modes for RP chromatography. Spectral features were extracted from the raw data using Progenesis QI v2.1 software. |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 275 °C |
| Spray Voltage: | 3.0 kV |
| MS ID: | MS001996 |
| Analysis ID: | AN002144 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Samples were analyzed in positive and negative ion modes for RP chromatography. Spectral features were extracted from the raw data using Progenesis QI v2.1 software. |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 275 °C |
| Spray Voltage: | -2.8 kV |
