Summary of Study ST001792

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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001792
Study TitleEffect of external low-dose rate radiation on mouse biofluid metabolomic signatures (part III)
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 Date2021-05-12
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

Select appropriate tab below to view additional metadata details:

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:SU001869
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Gender:Male
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Factor Factor
SA16693972Control D1
SA16694084Control D1
SA166941101Control D1
SA166942135Control D1
SA166943139Control D1
SA166944173Control D1
SA166945169Control D1
SA166946165Control D1
SA166947157Control D1
SA16694863Control D2
SA16694980Control D2
SA166950104Control D2
SA16695129Control D2
SA16695223Control D2
SA166953131Control D2
SA16695449Control D2
SA166955116Control D2
SA166956123Control D2
SA16695730Control D2
SA16695853Control D20
SA16695983Control D20
SA16696091Control D20
SA16696122Control D20
SA16696221Control D20
SA16696333Control D3
SA166964124Control D3
SA166965155Control D3
SA16696699Control D3
SA166967122Control D3
SA166968114Control D3
SA166969168Control D3
SA16697055Control D3
SA16697113Control D3
SA166972133Control D3
SA16697370Control D30
SA16697456Control D30
SA16697519Control D30
SA16697650Control D30
SA16697748Control D30
SA166978132Control D5
SA166979151Control D5
SA16698020Control D5
SA166981100Control D5
SA166982156Control D5
SA16698367Control D5
SA16698437Control D5
SA16698571Control D5
SA166986174Control D5
SA166987108Control D5
SA16698814HDR D1
SA166989106HDR D1
SA16699098HDR D1
SA166991148HDR D1
SA166992166HDR D1
SA16699382HDR D2
SA16699454HDR D2
SA16699564HDR D2
SA16699687HDR D2
SA166997121HDR D2
SA166998138HDR D3
SA16699932HDR D3
SA16700088HDR D3
SA167001175HDR D3
SA16700246HDR D3
SA167003158HDR D5
SA167004172HDR D5
SA167005117HDR D5
SA167006105HDR D5
SA16700736HDR D5
SA167008149LDR D1
SA167009115LDR D1
SA16701066LDR D1
SA16701190LDR D1
SA16701257LDR D1
SA16701397LDR D2
SA16701438LDR D2
SA16701581LDR D2
SA16701647LDR D2
SA16701774LDR D2
SA16701816LDR D20
SA16701973LDR D20
SA167020134LDR D20
SA167021118LDR D20
SA167022167LDR D20
SA16702389LDR D3
SA167024107LDR D3
SA167025125LDR D3
SA167026150LDR D3
SA167027152LDR D3
SA167028141LDR D30
SA16702939LDR D30
SA167030140LDR D30
SA16703140LDR D30
SA167032159LDR D30
SA16703331LDR D5
SA16703465LDR D5
SA167035142LDR D5
SA16703612LDR D5
SA16703715LDR D5
Showing results 1 to 99 of 99

Collection:

Collection ID:CO001862
Collection Summary:Serum was collected after irradiation
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR001882
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).

Sample Preparation:

Sampleprep ID:SP001875
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).
Processing Storage Conditions:-80℃

Combined analysis:

Analysis ID AN002907 AN002908
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:CH002155
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:MS002699
Analysis ID:AN002907
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
MS Comments:Negative and positive electrospray ionization (ESI) data-independent modes were used for data acquisition with leucine enkephalin ([M+H]+ = 556.2771, [M-H]- = 554.2615) as Lock-Spray®. 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:MS002700
Analysis ID:AN002908
Instrument Name:Waters Synapt G2
Instrument Type:QTOF
MS Type:ESI
MS Comments:Negative and positive electrospray ionization (ESI) data-independent modes were used for data acquisition with leucine enkephalin ([M+H]+ = 556.2771, [M-H]- = 554.2615) as Lock-Spray®. 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
  logo