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

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (Contains raw data)
Study IDST000133
Study Title1H NMR Metabolomics Study of Metastatic Melanoma in C57BL/6J Mouse Spleen
Study TypeTissue Extracts Comparison
Study SummaryTissue extracts from metastatic melanoma mouse spleen and controls were compared via NMR based metabolomic analysis
Institute
Pacific Northwest National Laboratory
DepartmentFundamental & Computational Sciences
Last NameHu
First NameJianzhi
Emailjianzhi.hu@pnnl.gov
Submit Date2015-01-08
Num Groups1
Total Subjects12
Raw Data AvailableYes
Raw Data File Type(s).fid, .loG, procpar, text
Uploaded File Size140 K
Analysis Type DetailNMR
Release Date2015-01-08
Release Version1
Jianzhi Hu Jianzhi Hu
https://dx.doi.org/10.21228/M8B594
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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
SA0073857B10No
SA0073867C10No
SA0073877D10No
SA0073887E 10No
SA0073897A10No
SA0073906E 10Yes
SA0073916B10Yes
SA0073926C10Yes
SA0073936D10Yes
SA0073946A10Yes
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.

Chromatography:

Chromatography ID:CH000147

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
  logo