Summary of Study ST000133
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 PR000118. The data can be accessed directly via it's Project DOI: 10.21228/M8B594 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000133 |
| Study Title | 1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen |
| Study Type | Tissue Extracts Comparison |
| Study Summary | Tissue extracts from metastatic melanoma mouse spleen and controls were compared via NMR based metabolomic analysis |
| Institute | Pacific Northwest National Laboratory |
| Department | Fundamental & Computational Sciences |
| Last Name | Hu |
| First Name | Jianzhi |
| jianzhi.hu@pnnl.gov | |
| Submit Date | 2015-01-08 |
| Num Groups | 1 |
| Total Subjects | 12 |
| Raw Data Available | Yes |
| Uploaded File Size | 140 K |
| Analysis Type Detail | NMR |
| Release Date | 2015-01-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000118 |
| Project DOI: | doi: 10.21228/M8B594 |
| Project Title: | 1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen |
| Institute: | Pacific Northwest National Laboratory |
| Department: | Fundamental & Computational Sciences |
| Last Name: | Hu |
| First Name: | Jianzhi |
| Email: | jianzhi.hu@pnnl.gov |
Subject:
| Subject ID: | SU000152 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Disease State |
|---|---|---|
| SA007385 | 7B10 | No |
| SA007386 | 7C10 | No |
| SA007387 | 7D10 | No |
| SA007388 | 7E 10 | No |
| SA007389 | 7A10 | No |
| SA007390 | 6E 10 | Yes |
| SA007391 | 6B10 | Yes |
| SA007392 | 6C10 | Yes |
| SA007393 | 6D10 | Yes |
| SA007394 | 6A10 | Yes |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO000136 |
| Collection Summary: | Spleens were dissected and snap-frozen at -80°C before NMR spectroscopy and morphology analysis. |
| Sample Type: | Tissue |
Treatment:
| Treatment ID: | TR000154 |
| Treatment Summary: | A total of 12 six-week-old C57BL/6J male mice at the age of week-7 the mice were randomly divided into two groups, an experimental group (n=7) that received subcutaneous injection with suspended 105 B16-F10 tumor cells at four flank locations on each leg, and a control group (n=5) that were injected with the same amount of PBS at same places. The animals were fed a standard diet and housed one mouse per cage and maintained in a temperature-controlled room (22-25°C, 45% humidity) on a 12:12h dark-light cycle. All mice, each of which was weighed weekly, were allowed free access to water and food before being sacrificed by CO2 asphyxiation at the age of fourteen weeks. |
Sample Preparation:
| Sampleprep ID: | SP000149 |
| Sampleprep Summary: | Cold Methanol/H2O/Chloroform Extraction |
| Extraction Method: | Step 1: The pre-weighted intact frozen tissue was homogenized in ice bath after adding 0.25 ml MeOH and 0.053 ml H2O for each sample containing 30 to 60 mg of tissue, followed by vortexing the mixture and then adding 0.125 ml chloroform, vortexing again. Step 2: 0.125 ml chloroform and 0.125 ml water was added to the sample and then vortexed again, followed by transferring different layers into glass vials separately with syringes after the mixture being left on ice for 15 min and centrifuged at 8000rpm for 2 min at 4°C. Finally, the solvents were removed by employing lyophilizer (MeOH/H2O layer, hydrophilic metabolites) or by evaporating under dry nitrogen gas (CHCl3 layer, hydrophobic metabolites). The extracts were then stored at -80°C before performing NMR measurements. |
Analysis:
| Analysis ID: | AN000215 |
| Analysis Type: | NMR |
| Software Version: | Vnmrj/ 3.2; Chenomx/7.6 |
| Chromatography ID: | CH000147 |
| Num Factors: | 2 |
| Num Metabolites: | 74 |
NMR:
| NMR ID: | NM000049 |
| Analysis ID: | AN000215 |
| Instrument Name: | Varian |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D 1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5 mM |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | 5mm HCN probe with Z axis-gradient |
| NMR Solvent: | D2O/CDCl3 |
| NMR Tube Size: | 5mm * 8 in |
| Shimming Method: | Gradient shim |
| Pulse Sequence: | PRESAT |
| Water Suppression: | presat |
| Pulse Width: | 6.5 us |
| Receiver Gain: | 60 |
| Chemical Shift Ref Cpd: | TSP-d4 |
| Temperature: | 293 K |
| Number Of Scans: | 8192 |
| Dummy Scans: | 2 |
| Acquisition Time: | 1.9137 s |
| Relaxation Delay: | 2 |
| Spectral Width: | 10000 Hz |
| Num Data Points Acquired: | 38274 |
| Line Broadening: | 0.5 |
