Summary of Study ST000261
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 PR000212. The data can be accessed directly via it's Project DOI: 10.21228/M80C7B This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000261 |
| Study Title | 1H NMR metabolomics study of spleen from C57BL/6 mice exposed to gamma radiation |
| Study Type | Tissue Extracts Comparison |
| Study Summary | Tissue extracts from exposure to gamma radiation 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 |
| Address | -- |
| jianzhi.hu@pnnl.gov | |
| Phone | -- |
| Submit Date | 2015-10-26 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Uploaded File Size | 24M |
| Analysis Type Detail | NMR |
| Release Date | 2015-10-26 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000212 |
| Project DOI: | doi: 10.21228/M80C7B |
| Project Title: | 1H NMR metabolomics study of spleen from C57BL/6 mice exposed to gamma radiation |
| Project Summary: | 1H NMR metabolomics study of spleen from C57BL/6 mice exposed to gamma radiation |
| Institute: | Pacific Northwest National Laboratory |
| Department: | Fundamental & Computational Sciences |
| Last Name: | Hu |
| First Name: | Jianzhi |
| Address: | -- |
| Email: | jianzhi.hu@pnnl.gov |
| Phone: | -- |
Subject:
| Subject ID: | SU000281 |
| 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? (0, no; 1, yes) | Dosage (Gy) |
|---|---|---|---|
| SA011995 | P047 | 0 | 0 |
| SA011996 | P048 | 0 | 0 |
| SA011997 | P041 | 0 | 0 |
| SA011998 | P046 | 0 | 0 |
| SA011999 | P045 | 0 | 0 |
| SA012000 | P042 | 0 | 0 |
| SA012001 | P043 | 0 | 0 |
| SA012002 | P044 | 0 | 0 |
| SA012003 | P345 | 1 | 3 |
| SA012004 | P344 | 1 | 3 |
| SA012005 | P341 | 1 | 3 |
| SA012006 | P343 | 1 | 3 |
| SA012007 | P342 | 1 | 3 |
| SA012008 | P744 | 1 | 7.8 |
| SA012009 | P743 | 1 | 7.8 |
| SA012010 | P741 | 1 | 7.8 |
| SA012011 | P742 | 1 | 7.8 |
| Showing results 1 to 17 of 17 |
Collection:
| Collection ID: | CO000275 |
| Collection Summary: | Spleens were dissected and snap-frozen at -80°C before NMR spectroscopy and morphology analysis. |
| Sample Type: | Tissue |
Treatment:
| Treatment ID: | TR000295 |
| Treatment Summary: | A total of 17 seven-week-old C57BL/6 female mice were randomly grouped before total body being exposed to gamma irradiation using a high activity gamma source (1250 keV 60Co). The linear energy transfer (LET) associated with these fields is in the range of 0.2-2 keV/?m. For the total body gamma radiation, the animals were isolated to the corner of their polymer cages, placed at a minimum of 100 cm from the collimated 6000 Ci 60Co source, and then irradiated to the proposed dosage. The resulting absorbed dose rate at approximately 600 mg/cm2 depth was 0.83Gy/min relative to tissue. Groups of mice were exposed to radiation doses of 0Gy (control, n=8), 3.0Gy (n=5) and 7.8Gy (n=4). After 4 days post exposure, mice were sacrificed with 70/30 CO2/O2 . |
Sample Preparation:
| Sampleprep ID: | SP000289 |
| Sampleprep Summary: | Cold Methanol/H2O/Chloroform Extraction |
| Sampleprep Protocol Comments: | Extraction protocol: Step 1: Weight each intact frozen tissue and add 0.25 ml methanol and 0.053 ml deionized water for each sample, after homogenizing in ice bath using the Tissue Tearor (Model 985-370, BioSpec Products, Inc.), then following by vortexing the mixture and then adding 0.125 ml chloroform, vortexing again. Step 2: 0.125 ml chloroform and 0.125 ml deionized water were added to the sample and then vortexed again, following by transferring different layers into glass vials separately with syringes after the mixture being left on ice for 15 min and centrifuged at 6,000 rpm for 16 min at 4 °C. Finally, the MeOH/H2O layer solvents (hydrophilic metabolites) were removed by employing the lyophilizer. And the extracts were stored at ?80 °C freezer before performing NMR measurements. |
Analysis:
| Analysis ID: | AN000416 |
| Analysis Type: | NMR |
| Software Version: | Vnmrj/ 4.0; Chenomx/8.1 |
| Chromatography ID: | CH000293 |
| Num Factors: | 3 |
NMR:
| NMR ID: | NM000058 |
| Analysis ID: | AN000416 |
| Instrument Name: | Varian 600 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D |
| Spectrometer Frequency: | 600 MHZ |
| Power Level: | Deuterium |
| Receiver Gain: | 0.05 mM |
| Presaturation Power Level: | 5mm HCN probe with Z axis-gradient |
| Chemical Shift Ref Cpd: | D2O |
| Temperature: | 5mm * 8 in |
| Number Of Scans: | Gradient shim |
| Dummy Scans: | PRESAT |
| Acquisition Time: | presat |
| Relaxation Delay: | 7.5 us |
| Zero Filling: | DSS |
| Apodization: | 293 K |
| Baseline Correction Method: | 19968 |
