Summary of Study ST001791

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 PR001137. The data can be accessed directly via it's Project DOI: 10.21228/M8R102 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 IDST001791
Study TitleEffect of external low-dose rate radiation on mouse biofluid metabolomic signatures (part II)
Study SummaryAn important component of ionizing radiation (IR) exposure after a radiological incident may include low-dose rate (LDR) exposures either externally or internally, such as from 137Cs deposition. LDR exposures can have different effects compared to acute high-dose rate exposures from a health and biodosimetry perspective. In this study, a novel irradiation system, VAriable Dose-rate External 137Cs irradiatoR (VADER), was used to expose male and female mice to a variable LDR over a 30-day time span to cumulative doses of 1 (only in males), 2, 2.8, 4.1, 8.8 (only in males), or 9.7 Gy to simulate fall-out type exposures. Urine and serum from mice exposed to an acute dose (~0.8 Gy/min) of x-rays were collected in parallel. Radiation markers were identified by global mass spectrometry based metabolomics and the machine learning algorithm Random Forests.
Institute
Georgetown University
Last NamePannkuk
First NameEvan
Address3970 Reservoir Rd, NW New Research Building E504
Emailelp44@georgetown.edu
Phone2026875650
Submit Date2021-05-11
Raw Data AvailableYes
Raw Data File Type(s)raw(Waters)
Analysis Type DetailLC-MS
Release Date2021-12-15
Release Version1
Evan Pannkuk Evan Pannkuk
https://dx.doi.org/10.21228/M8R102
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001137
Project DOI:doi: 10.21228/M8R102
Project Title:Effect of external low-dose rate (LDR) radiation on mouse biofluid metabolomic
Project Summary:An important component of ionizing radiation (IR) exposure after a radiological incident may include low-dose rate (LDR) exposures either externally or internally, such as from 137Cs deposition. LDR exposures can have different effects compared to acute high-dose rate exposures from a health and biodosimetry perspective. In this study, a novel irradiation system, VAriable Dose-rate External 137Cs irradiatoR (VADER), was used to expose male and female mice to a variable LDR over a 30-day time span to cumulative doses of 1 (only in males), 2, 2.8, 4.1, 8.8 (only in males), or 9.7 Gy to simulate fall-out type exposures. Urine and serum from mice exposed to an acute dose (~0.8 Gy/min) of x-rays were collected in parallel. Radiation markers were identified by global mass spectrometry based metabolomics and the machine learning algorithm Random Forests.
Institute:Georgetown University
Last Name:Pannkuk
First Name:Evan
Address:3970 Reservoir Rd, NW New Research Building E504
Email:elp44@georgetown.edu
Phone:2026875650

Subject:

Subject ID:SU001868
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Gender:Female
Animal Animal Supplier:Charles River

Factors:

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

mb_sample_id local_sample_id Factor Factor
SA166757115A post
SA16675863Control post
SA16675961Control post
SA166760159Control post
SA16676166Control post
SA166762107Control post
SA16676352Control post
SA166764116Control post
SA166765165Control post
SA16676648Control post
SA166767101Control post
SA166768112Control post
SA16676970Control post
SA166770151Control post
SA166771216Control post
SA166772150Control post
SA16677388Control post
SA166774144Control post
SA16677580Control post
SA166776143Control post
SA166777138Control post
SA16677874Control post
SA166779222Control post
SA166780193Control post
SA166781192Control post
SA166782231Control post
SA16678325Control post
SA16678424Control post
SA166785185Control post
SA16678640Control post
SA16678728Control post
SA16678822Control post
SA16678917Control post
SA166790241Control post
SA16679110Control post
SA166792184Control post
SA166793177Control post
SA166794238Control post
SA166795170Control post
SA16679627Control post
SA166797120Control post
SA166798125Control post
SA166799207Control post
SA16680038Control post
SA166801209Control post
SA166802130Control pre
SA16680395Control pre
SA166804139Control pre
SA16680594Control pre
SA166806182Control pre
SA166807113Control pre
SA16680891Control pre
SA166809202Control pre
SA166810141Control pre
SA166811103Control pre
SA166812105Control pre
SA166813126Control pre
SA166814196Control pre
SA166815140Control pre
SA166816104Control pre
SA1668179Control pre
SA166818137Control pre
SA166819100Control pre
SA16682068Control pre
SA16682139Control pre
SA166822234Control pre
SA16682344Control pre
SA166824164Control pre
SA166825145Control pre
SA16682636Control pre
SA166827168Control pre
SA16682816Control pre
SA166829172Control pre
SA166830237Control pre
SA166831169Control pre
SA16683254Control pre
SA166833229Control pre
SA16683478Control pre
SA16683565Control pre
SA16683655Control pre
SA166837198Control pre
SA166838219Control pre
SA16683962Control pre
SA166840228Control pre
SA166841146Control pre
SA16684257Control pre
SA16684386Control pre
SA166844176HDR post
SA166845132HDR post
SA166846157HDR post
SA166847190HDR post
SA166848166HDR post
SA166849189HDR post
SA166850153HDR post
SA16685193HDR post
SA16685241HDR post
SA166853215HDR post
SA16685489HDR post
SA166855232HDR post
SA166856223HDR post
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Collection:

Collection ID:CO001861
Collection Summary:Spot urine collected before and after irradiation
Sample Type:Urine
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001881
Treatment Summary:The VADER was designed to deliver controlled dose rates in the range 0.1 – 1 Gy/day to a cohort of up to 15 mice. The VADER uses ~0.5 Ci of retired 137Cs brachytherapy seeds that are arranged in two platters placed above and below a “mouse hotel”. The platters can be placed ~0.5 – 60 cm above and below the mouse hotel allowing implementation of time-variable dose rates. Offline dosimetry of the VADER was performed annually using a NIST traceable 10x6-6 ionization chamber (Radcal Corp., Monrovia, CA). Dose uniformity across the surface was measured using EBT3 film (Ashland, Covington, KY, USA) and the variation was 15% across the hotel. A lead and high-density concrete brick shield ensured minimal radiation doses to occupationally exposed personnel (operators) inside (< 0.1 mGy/wk) and outside the room (< 0.02 mGy/wk). The mouse hotel consists of an acrylic box (35 x 35 x 12 cm) allowing housing of ≤ 15 mice with bedding material and food/water ad libitum. Temperature (20 – 25°C), humidity (40 – 60%), airflow and lighting were fully controlled to required animal care standards (temperature/humidity sensor, HWg HTemp, TruePath Technologies Victor, NY). Environmental controls and monitoring were integrated into the mouse hotel for easy replacement in case of radiation damage. Mice were monitored in real time using a 180° fisheye ELP USB camera (Amazon). All animal experiments were approved by the Columbia University Institutional Animal Care and Use Committee (IACUC; approved protocol AAQ2410) and were conducted under all relevant federal and state guidelines. Male and female C57BL/6 mice ( Charles River Laboratories, Frederick, MD, USA) were irradiated in the VADER in two randomized batches (15 mice) loaded into mouse hotels (one hotel loaded into the VADER and one in the same room as a zero-dose control). Five mice per time point were irradiated in two back-to-back runs (run 1: 2, 3, or 5 d; run 2: 5, 20, or 30 d) to a total dose of 1 Gy (1 d), 2 Gy (2 d), 2.8 Gy (3 d), 4.1 Gy (5 d), 8.8 Gy (20 d), and 9.7 Gy (30 d) (Figure S1). Urine and serum were flash frozen and then stored at -80°C until shipped to Georgetown University Medical Center for analysis.

Sample Preparation:

Sampleprep ID:SP001874
Sampleprep Summary:Samples were prepared and analyzed as previously described.18, 19 Briefly, serum (5 μl) was deproteinized (195 μl 66% cold acetonitrile [ACN]) with internal standards (2 μM debrisoquine [M+H]+ = 176.1188; 30 μM 4-nitrobenzoic acid [M-H]- = 166.0141), vortexed, incubated on ice (10 min), and centrifuged for 10 min (max speed, 4 °C). Urine (20 μl) was deproteinized (80 μl 50% cold ACN) and prepared as above. For urine and serum 1 μl of each sample were combined for a quality control (QC) sample.

Combined analysis:

Analysis ID AN002905 AN002906
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (50 x 2.1mm,1.7um) Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt G2 Waters Synapt G2
Ion Mode POSITIVE NEGATIVE
Units peak area peak area

Chromatography:

Chromatography ID:CH002154
Chromatography Summary:Mobile phases consisted of the following: solvent A (water/0.1% formic acid [FA]), solvent B (ACN/0.1% FA), solvent C (isopropanol [IPA]/ACN (90:10)/0.1% FA). The gradient for urine was (solvent A and B) 4.0 min 5% B, 4.0 min 20% B, 5.1 min 95% B, and 1.9 min 5% B at a flow rate of 0.5 ml/min. The gradient for serum was (solvent A, B, and C) 4.0 min 98:2 A:B, 4.0 min 40:60 A:B, 1.5 min 2:98 A:B, 2.0 min 2:98 A:C, 0.5 min 50:50 A:C, and 1.0 min 98:2 A:B at a flow rate of 0.5 ml/min.
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (50 x 2.1mm,1.7um)
Flow Gradient:The gradient for urine was (solvent A and B) 4.0 min 5% B, 4.0 min 20% B, 5.1 min 95% B, and 1.9 min 5% B at a flow rate of 0.5 ml/min. The gradient for serum was (solvent A, B, and C) 4.0 min 98:2 A:B, 4.0 min 40:60 A:B, 1.5 min 2:98 A:B, 2.0 min 2:98 A:C, 0.5 min 50:50 A:C, and 1.0 min 98:2 A:B at a flow rate of 0.5 ml/min.
Flow Rate:0.5 ml/min
Solvent A:100% water; 0.1% formic acid
Solvent B:solvent B:100% acetonitrile; 0.1% formic acid solvent C:90% isopropanol/10% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS002697
Analysis ID:AN002905
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
MS Comments:Operating conditions for ESI were: capillary voltage 2.75 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 1000 L/Hr.
Ion Mode:POSITIVE
  
MS ID:MS002698
Analysis ID:AN002906
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
MS Comments:Operating conditions for ESI were: capillary voltage 2.75 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 1000 L/Hr.
Ion Mode:NEGATIVE
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