Summary of Study ST000359
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 PR000285. The data can be accessed directly via it's Project DOI: 10.21228/M82W27 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000359 |
| Study Title | Broad Spectrum MS analysis of mouse microglia cells from Anxiety Prone HSV-Latently Infected Obese Mice |
| Study Type | Broad Spectrum LCMS |
| Study Summary | A mouse model of obese HSV-1 latent infection was developed. Broad spectrum metabolomics analysis was performed to better understand the metabolomic profile of microglia cells and to compare this metabolomics profile with that of the hippocampus, hypothalamus, and peripheral blood mononuclear cells. Microglia cell samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and microglia cell samples were collected and processed for metabolomics. |
| Institute | University of North Carolina |
| Department | Discovery Sciences |
| Laboratory | Sumner Lab |
| Last Name | Sumner |
| First Name | Susan |
| Address | Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081 |
| susan_sumner @unc.edu | |
| Phone | 704-250-5066 |
| Submit Date | 2016-03-05 |
| Num Groups | 4 |
| Total Subjects | 31 |
| Num Males | 31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Waters) |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-03-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000285 |
| Project DOI: | doi: 10.21228/M82W27 |
| Project Title: | Metabolic Profiling of Anxiety Prone HSV-Latently Infected Obese Mice |
| Project Type: | Broad Spectrum LCMS |
| Project Summary: | The biological factors that lead children from low socioeconomic backgrounds to be at greater risk for the development of anxiety and learning problems are not well understood. While it is clear that there are genetic components to the risk of developing mental health disorders, a role for environmental factors in inducing these problems has been suggested. Many of these factors that affect the brain likely involve exposures that occur early in life. Two such factors are the higher rates of herpes simplex virus (HSV)-1 seropositivity and prevalence of obesity among these children. HSV-1 infection has been associated with impaired cognition during childhood and mental health problems in adulthood. Additionally, obese adults are shown to have higher HSV-1 titers. Similarly, other studies have correlated a diet high in saturated fat and obesity with increased risk of mood disorders and anxiety. A mouse model of obese HSV-1 latent infection was developed. Broad spectrum metabolomics analysis was performed to better understand the metabolomic profile of hippocampus and to compare this metabolomics profile with that of the hypothalamus, microglia, and peripheral blood mononuclear cells. Brain tissue samples for metabolomics experiments were generated in the following manner: 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics. |
| Institute: | University of North Carolina at Chapel Hill |
| Department: | Gillings School of Public Health |
| Laboratory: | Department of Nutrition |
| Last Name: | Sheridan |
| First Name: | Patricia |
| Address: | 2002 Hooker Research Center, CB#7461, Chapel Hill NC, 27599 |
| Email: | patricia_sheridan@med.unc.edu |
| Phone: | 919-843-6434 |
| Funding Source: | NIH, Common Fund, Pilot and Feasibility |
Subject:
| Subject ID: | SU000380 |
| Subject Type: | mouse |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6 |
| Age Or Age Range: | 5.5 mo |
| Weight Or Weight Range: | 29.1 g-49.2 g |
| Gender: | male |
| Animal Animal Supplier: | JAX |
| Animal Housing: | 4/cage |
| Animal Feed: | Purina chow |
| Species Group: | Mammals |
Factors:
Subject type: mouse; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | HSV-1 | Diet at Week 2 |
|---|---|---|---|
| SA015953 | Total_Pool_04 | - | - |
| SA015954 | Total_Pool_05 | - | - |
| SA015955 | Total_Pool_03 | - | - |
| SA015956 | Total_Pool_01 | - | - |
| SA015957 | Total_Pool_02 | - | - |
| SA015962 | Micro418 | no | HF |
| SA015963 | Micro420 | no | HF |
| SA015964 | Micro419 | no | HF |
| SA015965 | Micro417 | no | HF |
| SA015958 | Micro446 | No | HF |
| SA015959 | Micro445 | No | HF |
| SA015960 | Micro443 | No | HF |
| SA015961 | Micro444 | No | HF |
| SA015966 | Micro421 | no | LF |
| SA015967 | Micro434 | no | LF |
| SA015968 | Micro431 | no | LF |
| SA015969 | Micro423 | no | LF |
| SA015970 | Micro422 | no | LF |
| SA015971 | Micro432 | no | LF |
| SA015972 | Micro424 | no | LF |
| SA015973 | Micro433 | no | LF |
| SA015974 | Micro426 | yes | HF |
| SA015975 | Micro442 | yes | HF |
| SA015976 | Micro425 | yes | HF |
| SA015977 | Micro439 | yes | HF |
| SA015978 | Micro441 | yes | HF |
| SA015979 | Micro427 | yes | HF |
| SA015980 | Micro440 | yes | HF |
| SA015981 | Micro438 | yes | LF |
| SA015982 | Micro435 | yes | LF |
| SA015983 | Micro430 | yes | LF |
| SA015984 | Micro436 | yes | LF |
| SA015985 | Micro429 | yes | LF |
| SA015986 | Micro437 | yes | LF |
| SA015987 | Micro428 | yes | LF |
| Showing results 1 to 35 of 35 |
Collection:
| Collection ID: | CO000374 |
| Collection Summary: | For extraction, 500 µL of an ice-cold solution of 90:10 Methanol:Chloroform (v/v) ¬was added to the tubes containing the thawed cell pellets. MagNA lyser ceramic beads were added to the tubes, and a MagNA lyser was used to beat the samples for two 30 seconds pulses at 2,000 rpm placing samples on cold block for 5 min in between pulses. Sonication for 5 min was performed to the beaten cell samples, followed by centrifugation at room temperature and at 16,000rcf for 4 min. A 350 µL aliquot of each experimental cell sample homogenized supernatant was transferred to a labeled 2.0 mL Lo-Bind Eppendorf tube |
| Sample Type: | brain homogenate |
Treatment:
| Treatment ID: | TR000394 |
| Treatment Summary: | 3-week old mice were placed on a 10% low fat (LF) diet and acclimated for one week prior to intranasal HSV-1 infection or mock infection with PBS. Fourteen days post-infection mice were randomized to either a 45% high fat diet (HF) or remained on the LF diet. Eight weeks post-diet transition, mice were euthanized and brain tissue samples were collected and processed for metabolomics. |
Sample Preparation:
| Sampleprep ID: | SP000387 |
| Sampleprep Summary: | For extraction, 500 µL of an ice-cold solution of 90:10 Methanol:Chloroform (v/v) ¬was added to the tubes containing the thawed cell pellets. MagNA lyser ceramic beads were added to the tubes, and a MagNA lyser was used to beat the samples for two 30 seconds pulses at 2,000 rpm placing samples on cold block for 5 min in between pulses. Sonication for 5 min was performed to the beaten cell samples, followed by centrifugation at room temperature and at 16,000rcf for 4 min. A 350 µL aliquot of each experimental cell sample homogenized supernatant was transferred to a labeled 2.0 mL Lo-Bind Eppendorf tube Analytical pooled samples were created by combining a 125 µL aliquot from each experimental sample in a labeled 20 mL glass vial. The QC pooled sample was vortexed for 30 sec and 350 µL aliquots were transferred to 5 labeled 2.0 mL Lo-Bind eppendorf tubes. Next, the supernatants of the study and QC pooled samples were dried overnight using a lyophilizer. The residue was reconstituted in 50 µL of reconstitution buffer (95:5 Water:Methanol, v/v) and mixed on an analog vortex mixer for 1 min with speed set at 10. Then, the samples were centrifuged at room temperature for 4 min at 16,000 rcf, and the supernatants were transferred to autosampler vials for data acquisition. |
Combined analysis:
| Analysis ID | AN000588 | AN000589 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Synapt G2 Si ESI-Q-TOF | Synapt G2 Si ESI-Q-TOF |
| Column | Waters ACQUITY UPLC HSS T3 | Waters ACQUITY UPLC HSS T3 |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Waters Synapt-G2-Si | Waters Synapt-G2-Si |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | intensity | intensity |
Chromatography:
| Chromatography ID: | CH000422 |
| Chromatography Summary: | UPLC-MS spectra were collected for all samples. UPLC was performed on a Waters Acquity UPLC with an Acquity HSS T3 column (2.1x 100mm x 1.8 µm) at 50 °C using the reversed-phase separation. Water with 0.1% formic acid (mobile phase A) and methanol with 0.1% formic acid (mobile phase B) were used as mobile phases and the metabolites were chromatographically separated using a gradient separation: (see the 3. Sheridan-Mice-Microglia Cells_RP-Metadata and Analytical Metadata.xlsx file for the flow gradient). Mass spectroscopy analysis was performed using a Synapt G2 Si ESI-Q-TOF using a 10 µL injection volume. UPLC-MS data were collected over 70-1000 m/z in both positive and negative modes. |
| Methods Filename: | RTI-RCMRC-RP |
| Instrument Name: | Synapt G2 Si ESI-Q-TOF |
| Column Name: | Waters ACQUITY UPLC HSS T3 |
| Flow Rate: | .4ml/min |
| Injection Temperature: | 8 C |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000524 |
| Analysis ID: | AN000588 |
| Instrument Name: | Waters Synapt-G2-Si |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | RTI-RCMRC-RP-POS |
| MS ID: | MS000525 |
| Analysis ID: | AN000589 |
| Instrument Name: | Waters Synapt-G2-Si |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | RTI-RCMRC-RP-NEG |
