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 ID	ST001791
Study Title	Effect of external low-dose rate radiation on mouse biofluid metabolomic signatures (part II)
Study 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
Submit Date	2021-05-11
Raw Data Available	Yes
Raw Data File Type(s)	raw(Waters)
Analysis Type Detail	LC-MS
Release Date	2021-12-15
Release Version	1

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:	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
SA166757	115	A	post
SA166758	63	Control	post
SA166759	61	Control	post
SA166760	159	Control	post
SA166761	66	Control	post
SA166762	107	Control	post
SA166763	52	Control	post
SA166764	116	Control	post
SA166765	165	Control	post
SA166766	48	Control	post
SA166767	101	Control	post
SA166768	112	Control	post
SA166769	70	Control	post
SA166770	151	Control	post
SA166771	216	Control	post
SA166772	150	Control	post
SA166773	88	Control	post
SA166774	144	Control	post
SA166775	80	Control	post
SA166776	143	Control	post
SA166777	138	Control	post
SA166778	74	Control	post
SA166779	222	Control	post
SA166780	193	Control	post
SA166781	192	Control	post
SA166782	231	Control	post
SA166783	25	Control	post
SA166784	24	Control	post
SA166785	185	Control	post
SA166786	40	Control	post
SA166787	28	Control	post
SA166788	22	Control	post
SA166789	17	Control	post
SA166790	241	Control	post
SA166791	10	Control	post
SA166792	184	Control	post
SA166793	177	Control	post
SA166794	238	Control	post
SA166795	170	Control	post
SA166796	27	Control	post
SA166797	120	Control	post
SA166798	125	Control	post
SA166799	207	Control	post
SA166800	38	Control	post
SA166801	209	Control	post
SA166802	130	Control	pre
SA166803	95	Control	pre
SA166804	139	Control	pre
SA166805	94	Control	pre
SA166806	182	Control	pre
SA166807	113	Control	pre
SA166808	91	Control	pre
SA166809	202	Control	pre
SA166810	141	Control	pre
SA166811	103	Control	pre
SA166812	105	Control	pre
SA166813	126	Control	pre
SA166814	196	Control	pre
SA166815	140	Control	pre
SA166816	104	Control	pre
SA166817	9	Control	pre
SA166818	137	Control	pre
SA166819	100	Control	pre
SA166820	68	Control	pre
SA166821	39	Control	pre
SA166822	234	Control	pre
SA166823	44	Control	pre
SA166824	164	Control	pre
SA166825	145	Control	pre
SA166826	36	Control	pre
SA166827	168	Control	pre
SA166828	16	Control	pre
SA166829	172	Control	pre
SA166830	237	Control	pre
SA166831	169	Control	pre
SA166832	54	Control	pre
SA166833	229	Control	pre
SA166834	78	Control	pre
SA166835	65	Control	pre
SA166836	55	Control	pre
SA166837	198	Control	pre
SA166838	219	Control	pre
SA166839	62	Control	pre
SA166840	228	Control	pre
SA166841	146	Control	pre
SA166842	57	Control	pre
SA166843	86	Control	pre
SA166844	176	HDR	post
SA166845	132	HDR	post
SA166846	157	HDR	post
SA166847	190	HDR	post
SA166848	166	HDR	post
SA166849	189	HDR	post
SA166850	153	HDR	post
SA166851	93	HDR	post
SA166852	41	HDR	post
SA166853	215	HDR	post
SA166854	89	HDR	post
SA166855	232	HDR	post
SA166856	223	HDR	post

Showing page 1 of 2 Results: 1 2 Next Showing results 1 to 100 of 182

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.

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.

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 S QTOF	Waters Synapt G2 S QTOF
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 S QTOF
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 S QTOF
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