Summary of Study ST001333

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 PR000910. The data can be accessed directly via it's Project DOI: 10.21228/M82H5K 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.

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Study IDST001333
Study TitleHuntington’s Disease Genotype Suppresses Global Manganese-Responsive Processes
Study TypeUntargeted metabolomics analysis
Study SummaryGlobal untargeted metabolomics studies performed in the striatum tissue, the brain region most sensitive to neurodegeneration in Huntington’s Disease, to investigate global Mn-dependent and Mn-responsive biology following various Mn exposures in a mouse model of HD.
Institute
Vanderbilt University
DepartmentChemistry
LaboratoryCenter for Innovative Technology
Last NameCodreanu
First NameSimona
Address1234 Stevenson Center Lane
Emailsimona.codreanu@vanderbilt.edu
Phone6158758422
Submit Date2020-03-27
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-09-29
Release Version1
Simona Codreanu Simona Codreanu
https://dx.doi.org/10.21228/M82H5K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000910
Project DOI:doi: 10.21228/M82H5K
Project Title:Huntington’s Disease Genotype Suppresses Global Manganese-Responsive Processes
Project Type:Untargeted Metabolomics analysis
Project Summary:Global untargeted metabolomics studies performed in the striatum tissue, the brain region most sensitive to neurodegeneration in Huntington’s Disease, to investigate global Mn-dependent and Mn-responsive biology following various Mn exposures in a mouse model of HD.
Institute:Vanderbilt University
Department:Chemistry
Laboratory:Center for Innovative Technology
Last Name:Codreanu
First Name:Simona
Address:1234 Stevenson Center Lane
Email:simona.codreanu@vanderbilt.edu
Phone:6158758422

Subject:

Subject ID:SU001407
Subject Type:Other
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:YAC128 and wildtype (WT)
Age Or Age Range:12 week and 32 week
Gender:Male and female

Factors:

Subject type: Other; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Sex Genotype Treatment Dosage
SA096584100_1833_C_F_128_0F 128 -
SA09658528_1856_C_F_128_0F 128 -
SA096586104_1874_C_F_128_0F 128 -
SA096587140_1949_A_F_128_0F 128 -
SA09658888_1919_C_F_128_0F 128 -
SA09658990_1893_C_F_128_0F 128 -
SA096590134_1928_A_F_128_0F 128 -
SA09659118_1976_A_F_128_0F 128 -
SA096592126_1954_C_F_128_0F 128 -
SA09659316_1986_A_F_128_0F 128 -
SA09659411_1984_A_F_128_0F 128 -
SA09659544_1890_A_F_128_0F 128 -
SA096596116_1879_C_F_128_15F 128 15
SA09659773_1864_C_F_128_15F 128 15
SA0965987_1909_C_F_128_15F 128 15
SA0965999_1964_C_F_128_15F 128 15
SA096600124_1843b_C_F_128_15F 128 15
SA09660110_1921_C_F_128_15F 128 15
SA09660242_1907_C_F_128_5F 128 5
SA09660340_1963_C_F_128_5F 128 5
SA09660462_1920_C_F_128_5F 128 5
SA096605135_1857_C_F_128_5F 128 5
SA0966061_1841_C_F_128_5F 128 5
SA09660785_1877_C_F_128_5F 128 5
SA096608114_1885_C_F_128_5F 128 5
SA09660934_1987_A_F_128_50F 128 50
SA09661060_1923_C_F_128_50F 128 50
SA096611111_1847_C_F_128_50F 128 50
SA09661292_1937_A_F_128_50F 128 50
SA09661319_1985_A_F_128_50F 128 50
SA096614123_1867_C_F_128_50F 128 50
SA09661536_1965_C_F_128_50F 128 50
SA096616105_1939_A_F_128_50F 128 50
SA096617141_1950_A_F_128_50F 128 50
SA09661839_1891_C_F_128_50F 128 50
SA09661980_1869_C_F_WT_0F WT -
SA096620122_1922_A_F_WT_0F WT -
SA09662175_1894_A_F_WT_0F WT -
SA09662252_1955_C_F_WT_0F WT -
SA096623117_1887_C_F_WT_0F WT -
SA09662449_1908_A_F_WT_0F WT -
SA09662555_1849_C_F_WT_0F WT -
SA096626119_1933_C_F_WT_0F WT -
SA09662724_1905_A_F_WT_0F WT -
SA09662848_1951_A_F_WT_0F WT -
SA09662979_1828_C_F_WT_15F WT 15
SA09663086_1865_C_F_WT_15F WT 15
SA09663122_1848_C_F_WT_15F WT 15
SA09663268_1842_C_F_WT_15F WT 15
SA09663337_1876_C_F_WT_15F WT 15
SA09663487_1875_C_F_WT_5F WT 5
SA096635127_1843_C_F_WT_5F WT 5
SA09663694_1855_C_F_WT_5F WT 5
SA09663793_1886_C_F_WT_5F WT 5
SA096638133_1827_C_F_WT_5F WT 5
SA0966393_1906_A_F_WT_50F WT 50
SA096640115_1918_A_F_WT_50F WT 50
SA0966414_1910_A_F_WT_50F WT 50
SA09664250_1850_C_F_WT_50F WT 50
SA09664333_1884_C_F_WT_50F WT 50
SA09664469_1834_C_F_WT_50F WT 50
SA09664525_1929_A_F_WT_50F WT 50
SA096646121_1943_A_F_WT_50F WT 50
SA096647108_1878_C_F_WT_50F WT 50
SA09664878_1866_C_F_WT_50F WT 50
SA096649109_1980_A_M_128_0M 128 -
SA09665017_1983_A_M_128_0M 128 -
SA09665198_1972_A_M_128_0M 128 -
SA096652137_1945_A_M_128_0M 128 -
SA09665371_1917_A_M_128_0M 128 -
SA09665414_1966_A_M_128_0M 128 -
SA096655101_1903_C_M_128_0M 128 -
SA09665676_1822_C_M_128_0M 128 -
SA09665761_1837_C_M_128_0M 128 -
SA09665841_1796_C_M_128_0M 128 -
SA09665966_1830_C_M_128_15M 128 15
SA09666026_1809_C_M_128_15M 128 15
SA09666145_1896_C_M_128_15M 128 15
SA09666258_1904_C_M_128_15M 128 15
SA09666365_1930_C_M_128_15M 128 15
SA09666456_1845_C_M_128_5M 128 5
SA09666572_1901_C_M_128_5M 128 5
SA09666654_1871_C_M_128_5M 128 5
SA0966678_1958_C_M_128_5M 128 5
SA096668110_1818_C_M_128_5M 128 5
SA096669103_1953_A_M_128_50M 128 50
SA0966702_1982_A_M_128_50M 128 50
SA09667130_1811_C_M_128_50M 128 50
SA09667297_1938_A_M_128_50M 128 50
SA096673132_1899_C_M_128_50M 128 50
SA09667482_1831_C_M_128_50M 128 50
SA09667512_1974_A_M_128_50M 128 50
SA09667670_1915_C_M_128_50M 128 50
SA09667767_1978_A_M_128_50M 128 50
SA096678112_1861_C_M_128_50M 128 50
SA09667915_1967_A_M_128_50M 128 50
SA096680106_1956_C_M_WT_0M WT -
SA09668151_1973_A_M_WT_0M WT -
SA096682120_1961_A_M_WT_0M WT -
SA096683139_1948_A_M_WT_0M WT -
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Collection:

Collection ID:CO001402
Collection Summary:For the single injection exposure, mice were sacrificed either 0, 1, 4, 12 or 24 hours after the injection to examine acute changes to Mn. For 1-week and 20-week Mn exposures, mice were sacrificed 24 hours after the final injection. For all studies, mice were sacrificed by cervical dislocation without anesthesia. Mice were decapitated with sharp scissors and the brain removed. The striatum was dissected out under a dissecting microscope, flash-frozen in liquid nitrogen and stored at -80C until later analysis.
Sample Type:Brain

Treatment:

Treatment ID:TR001422
Treatment Summary:This study utilized three Mn exposure paradigms: 1) a single subcutaneous exposure of either a 1% solution of MnCl2•4(H2O) in filtered MilliQ water at 50 mg/kg body weight or vehicle (filtered water), 2) a 1-week, and 3) 20-week chronic exposure. The 1-week exposure is a previously published week-long exposure protocol (intermittent injections given on days 0, 3 and 6, with sacrifice on day 7) known to elevate brain Mn levels1. The 20-week exposure is a twice weekly injection (Mondays and Thursdays) based on the estimated half-life of 3.5 days for Mn administered via this route and pilot work suggesting the absence of observable toxicity with this exposure paradigm (including no weight loss or physical signs of distress).
Treatment Compound:Mn
Treatment Dose:0, 5, 15, 50 mg/kg body weight

Sample Preparation:

Sampleprep ID:SP001415
Sampleprep Summary:Previously frozen striatal tissue was lysed in 400µL ice-cold lysing buffer (1:1:2, ACN:MeOH:Ammonium Bicarbonate (0.1M, pH 8.0) (LC-MS grade). Individual samples were sonicated using a probe tip sonicator, 10 pulses, at 30% power and cooled down on ice between samples. A BCA protein assay was used to determine the protein concentration for each individual sample, and adjusted to a total amount of protein of 200µg in 200 µL of lysis buffer. Isotopically labeled standards, Creatinine-D3 and Lysine-D4, were added to each sample to assess sample processing steps (metabolite extraction and reconstitution). Following lysis and standard addition, protein precipitation was performed by adding 800µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min to eliminate proteins. The supernatants containing metabolites were dried via speed-vacuum. Dried metabolite extracts were stored frozen at -80C until ready to use. Prior to mass spectrometry analysis, extracts were reconstituted in 100 μl of acetonitrile/ water (80:20, v/v) and centrifuged for 5 min at 15K rpm to remove insoluble material. Quality control samples were prepared by pooling equal volumes of each sample. Isotopically labeled standards, Valine-D8 and Inosine-4N15, were added to each sample to determine MS instrument reproducibility.
Sampleprep Protocol Filename:Codreags00_20200327_075634_PR_MS_Metabolomics_Protocol.pdf
Processing Storage Conditions:-80℃
Extraction Method:Following lysis and standard addition, protein precipitation was performed by adding 800µL of ice-cold methanol (4x by volume). Samples were incubated at -80°C overnight. Following incubation, samples were centrifuged at 10,000 rpm for 10 min to eliminate proteins. The supernatants containing metabolites were dried via speed-vacuum.
Extract Storage:-80℃
Sample Resuspension:100 μl of acetonitrile/ water (80:20, v/v) and centrifuged for 5 min at 15K rpm to remove insoluble material
Sample Spiking:Valine-D8 and Inosine-4N15, were added to each sample to determine MS instrument reproducibility.

Combined analysis:

Analysis ID AN002222
Analysis type MS
Chromatography type HILIC
Chromatography system Vanquish UHPLC binary system
Column SeQuant ZIC-HILIC (100 x 2.1mm,3.5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH001630
Instrument Name:Vanquish UHPLC binary system
Column Name:SeQuant ZIC-HILIC (100 x 2.1mm,3.5um)
Column Temperature:40
Flow Rate:0.2 mL/min
Solvent A:90% water/10% acetonitrile; 5 mM ammonium formate
Solvent B:90% acetonitrile/10% water; 5 mM ammonium formate
Chromatography Type:HILIC

MS:

MS ID:MS002068
Analysis ID:AN002222
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Ultra-performance liquid chromatography - tandem mass spectrometry (UPLC-MS/MS and UPLC-MS) raw data were imported, processed, normalized and reviewed using Progenesis QI v.2.1 (Non-linear Dynamics, Newcastle, UK).
Ion Mode:POSITIVE
Analysis Protocol File:Codreags00_20200327_075634_PR_MS_Metabolomics_Protocol.pdf
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