Summary of Study ST003000

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 PR001870. The data can be accessed directly via it's Project DOI: 10.21228/M80M84 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 IDST003000
Study TitleEffects of Microbiome Depletion on Radiation Biodosimetry Metabolomics
Study SummaryDevelopment of novel biodosimetry assays and medical countermeasures is needed to obtain a level of radiation preparedness in the event of malicious or accidental mass exposures to ionizing radiation (IR). For biodosimetry, metabolic profiling with mass spectrometry (MS) platforms has identified several small molecules in easily accessible biofluids that are promising for dose reconstruction. As our microbiome has profound effects on biofluid metabolite composition, it is of interest how variation in the host microbiome may affect metabolomics based biodosimetry. Here, we chemically ‘knocked out’ the microbiome of male and female C57BL/6 mice (Abx mice) and then irradiated (0, 3, or 8 Gy) them to determine the role of the host microbiome on biofluid radiation signatures (3 d serum).
Institute
Georgetown University
Last NamePannkuk
First NameEvan
Address3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA
Emailelp44@georgetown.edu
Phone2026875650
Submit Date2023-12-05
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2024-04-05
Release Version1
Evan Pannkuk Evan Pannkuk
https://dx.doi.org/10.21228/M80M84
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001870
Project DOI:doi: 10.21228/M80M84
Project Title:Effect of Antibiotic Administration on Metabolomic Radiation Biodosimetry
Project Summary:Development of novel biodosimetry assays and medical countermeasures is needed to obtain a level of radiation preparedness in the event of malicious or accidental mass exposures to ionizing radiation (IR). For biodosimetry, metabolic profiling with mass spectrometry (MS) platforms has identified several small molecules in easily accessible biofluids that are promising for dose reconstruction. As our microbiome has profound effects on biofluid metabolite composition, it is of interest how variation in the host microbiome may affect metabolomics based biodosimetry. Here, we chemically ‘knocked out’ the microbiome of male and female C57BL/6 mice (Abx mice) and then irradiated (0, 3, or 8 Gy) them to determine the role of the host microbiome on biofluid radiation signatures (3 d serum).
Institute:Georgetown University
Last Name:Pannkuk
First Name:Evan
Address:3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA
Email:elp44@georgetown.edu
Phone:2026875650

Subject:

Subject ID:SU003113
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Antibiotics Irradiation
SA3265007596Mw 0Gy
SA3265017633Fw 0Gy
SA3265027598Mw 0Gy
SA3265037631Fw 0Gy
SA3265047635Fw 0Gy
SA3265057594Mw 0Gy
SA3265067634Fw 0Gy
SA3265077595Mw 0Gy
SA3265087632Fw 0Gy
SA3265097597Mw 0Gy
SA3265107640Fw 3Gy
SA3265117603Mw 3Gy
SA3265127601Mw 3Gy
SA3265137602Mw 3Gy
SA3265147637Fw 3Gy
SA3265157638Fw 3Gy
SA3265167639Fw 3Gy
SA3265177636Fw 3Gy
SA3265187600Mw 3Gy
SA3265197599Mw 3Gy
SA3265207643Fw 8Gy
SA3265217641Fw 8Gy
SA3265227608Mw 8Gy
SA3265237644Fw 8Gy
SA3265247650Fw 8Gy
SA3265257605Mw 8Gy
SA3265267607Mw 8Gy
SA3265277642Fw 8Gy
SA3265287604Mw 8Gy
SA3265297606Mw 8Gy
SA3265307583Mwo 0Gy
SA3265317617Fwo 0Gy
SA3265327619Fwo 0Gy
SA3265337616Fwo 0Gy
SA3265347582Mwo 0Gy
SA3265357579Mwo 0Gy
SA3265367618Fwo 0Gy
SA3265377581Mwo 0Gy
SA3265387614Fwo 0Gy
SA3265397585Mwo 3Gy
SA3265407621Fwo 3Gy
SA3265417624Fwo 3Gy
SA3265427625Fwo 3Gy
SA3265437586Mwo 3Gy
SA3265447588Mwo 3Gy
SA3265457623Fwo 3Gy
SA3265467622Fwo 3Gy
SA3265477587Mwo 3Gy
SA3265487628Fwo 8Gy
SA3265497626Fwo 8Gy
SA3265507593Mwo 8Gy
SA3265517589Mwo 8Gy
SA3265527590Mwo 8Gy
SA3265537591Mwo 8Gy
SA3265547630Fwo 8Gy
SA3265557592Mwo 8Gy
SA3265567627Fwo 8Gy
SA3265577629Fwo 8Gy
Showing results 1 to 58 of 58

Collection:

Collection ID:CO003106
Collection Summary:On day 3, mice were euthanized by CO2 inhalation, blood was collected by cardiac puncture, and tissues were collected. Tissues were flash frozen. Serum samples were prepared using BD Microtainer Tube (REF 365967) with ~100 µL of whole blood added to each tube, kept at room temperature for 30 min, then spun at 1300× g at 4 °C for 10 min. All tissues and biofluids were stored at −80 °C until analysis.
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR003122
Treatment Summary:We used 8 week old male and female C57BL/6 mice that were purchased from Charles River Laboratories (Frederick, MD) and were assigned to sham, 3 Gy, or 8 Gy cohorts. A control group (Abx-con) did not receive antibiotics in drinking water and a treatment group (Abx) received broad-spectrum antibiotics (n=10 per group, half male half female) (S1 Fig). Mice were provided with deionized water ad libitum either with or without the antibiotic cocktail (enrofloxacin [0.575 mg/ml] and ampicillin [1 mg/ml]) for 8 days prior to irradiation [24]. Mice were irradiated in an acrylic, 12-slot mouse pie cage (MPC-1, Braintree Scientific, Braintree, MA) on top of a specimen turntable (XD1905-0000, Precision X-Ray Inc, Branford, CT) and 0, 3 or 8 Gy X-ray irradiated (1.67 Gy/min; X-Rad 320, Precision X-Ray Inc.; filter, 0.75 mm tin/ 0.25 mm copper/1.5 mm aluminum). For Abx-con mice, spot urines (>100 µL) were collected 1 d prior to irradiation and at 1 and 3 d post-irradiation (fecal samples collected 1 d prior to irradiation and at 3 d post-irradiation).

Sample Preparation:

Sampleprep ID:SP003119
Sampleprep Summary:On day 3, mice were euthanized by CO2 inhalation, blood was collected by cardiac puncture, and tissues were collected. Tissues were flash frozen. Serum samples were prepared using BD Microtainer Tube (REF 365967) with ~100 µL of whole blood added to each tube, kept at room temperature for 30 min, then spun at 1300× g at 4 °C for 10 min. All tissues and biofluids were stored at −80 °C until analysis.

Combined analysis:

Analysis ID AN004927 AN004928
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um) Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTRAP QTRAP
MS instrument name Waters Xevo-G2-S Waters Xevo-G2-S
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH003719
Chromatography Summary:The LC and MS conditions for serum was as follows: LC solvent A (water/0.1% formic acid [FA]), solvent B (acetonitrile/0.1% FA), and solvent C (isopropanol/0.1% FA). Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr. The gradient for serum was: 4 min 98% A 2% B, 4 min 40% A 60% B, 1.5 min 2% A 98% B, 2 min 11.8% B 88.2% C, 0.5 min 50% A 50% B, and 1 min 98% A 2% B at a flow rate of 0.5 ml/min, column temp 60 °C (S3 Fig).
Instrument Name:Waters Acquity
Column Name:Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)
Column Temperature:60
Flow Gradient:4 min 98% A 2% B, 4 min 40% A 60% B, 1.5 min 2% A 98% B, 2 min 11.8% B 88.2% C, 0.5 min 50% A 50% B, and 1 min 98% A 2% B
Flow Rate:0.5 ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
Solvent C:100% isopropanol; 0.1% formic acid

MS:

MS ID:MS004670
Analysis ID:AN004927
Instrument Name:Waters Xevo-G2-S
Instrument Type:QTRAP
MS Type:ESI
MS Comments:Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr.
Ion Mode:POSITIVE
  
MS ID:MS004671
Analysis ID:AN004928
Instrument Name:Waters Xevo-G2-S
Instrument Type:QTRAP
MS Type:ESI
MS Comments:Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr.
Ion Mode:NEGATIVE
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