Summary of Study ST003453

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 PR002127. The data can be accessed directly via it's Project DOI: 10.21228/M8PG19 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.

Study ID	ST003453
Study Title	Integration of Metabolomics and Transcriptomics Reveals Metabolic Characteristics and Potential Biomarker Involved in Radiation-Induced Liver Injury in a Rat Model.
Study Summary	Radiation-induced liver damage (RILD) is a disease characterized by a series of physiological and pathological changes in liver tissue following exposure to a certain dose of radiation, and it is also a common complication of liver cancer and abdominal tumor radiotherapy. To date, the pathogenesis of RILD remains unclear, and effective diagnostic and therapeutic approaches are lacking. Based on this, the present study established an animal model of radiation-induced liver disease (RILD) using whole-liver irradiated rats. Metabolomics and transcriptomics were integrated to analyze liver tissue samples collected 7 days post-irradiation. The involved metabolic disorders primarily include ammonia metabolism, amino acid metabolism, glutathione metabolism and lipid metabolism. Moreover, a panel of potential plasma metabolic markers was identified through correlation analysis between liver tissue and plasma metabolic characteristics. Subsequently, the levels of radiation injury within 7 days post irradiation were assessed. This study provides experimental evidence for the identification of early diagnostic markers for whole-liver irradiation and RILD, as well as for exploring the molecular and pathophysiological mechanisms of RILD.
Institute	Soochow University
Last Name	Wang
First Name	Chang
Address	Suzhou, No. 199, Renai Road, Suzhou Industrial Park
Email	wangchang@suda.edu.cn
Phone	+8651265880067
Submit Date	2024-08-16
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	GC/LC-MS
Release Date	2024-09-24
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002127
Project DOI:	doi: 10.21228/M8PG19
Project Title:	Integration of Metabolomics and Transcriptomics Reveals Metabolic Characteristics and Potential Biomarker Involved in Radiation-Induced Liver Injury in a Rat Model.
Project Type:	MS quantitative analysis
Project Summary:	Radiation-induced liver damage (RILD) is a disease characterized by a series of physiological and pathological changes in liver tissue following exposure to a certain dose of radiation, and it is also a common complication of liver cancer and abdominal tumor radiotherapy. To date, the pathogenesis of RILD remains unclear, and effective diagnostic and therapeutic approaches are lacking. Based on this, the present study established an animal model of radiation-induced liver disease (RILD) using whole-liver irradiated rats. Metabolomics and transcriptomics were integrated to analyze liver tissue samples collected 7 days post-irradiation. The involved metabolic disorders primarily include ammonia metabolism, amino acid metabolism, glutathione metabolism and lipid metabolism. Moreover, a panel of potential plasma metabolic markers was identified through correlation analysis between liver tissue and plasma metabolic characteristics. Subsequently, the levels of radiation injury within 7 days post irradiation were assessed. This study provides experimental evidence for the identification of early diagnostic markers for whole-liver irradiation and RILD, as well as for exploring the molecular and pathophysiological mechanisms of RILD.
Institute:	Soochow University
Last Name:	Wang
First Name:	Chang
Address:	Suzhou, No. 199, Renai Road, Suzhou Industrial Park
Email:	wangchang@suda.edu.cn
Phone:	+86-512-65880067

Subject:

Subject ID:	SU003581
Subject Type:	Mammal
Subject Species:	Rattus norvegicus
Gender:	Female

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Treatment	Batch
SA381547	20220917-POS-418-25-7D	Liver tissue	25GY	A
SA381548	20220917-NEG-403-25-7D	Liver tissue	25GY	A
SA381549	20220917-POS-477-25-7D	Liver tissue	25GY	A
SA381550	20220917-POS-475-25-7D	Liver tissue	25GY	A
SA381551	20220917-POS-451-25-7D	Liver tissue	25GY	A
SA381552	20220917-POS-444-25-7D	Liver tissue	25GY	A
SA381553	20220917-POS-442-25-7D	Liver tissue	25GY	A
SA381554	20220917-POS-412-25-7D	Liver tissue	25GY	A
SA381555	20220917-NEG-412-25-7D	Liver tissue	25GY	A
SA381556	20220917-NEG-442-25-7D	Liver tissue	25GY	A
SA381557	20220917-NEG-444-25-7D	Liver tissue	25GY	A
SA381558	20220917-NEG-451-25-7D	Liver tissue	25GY	A
SA381559	20220917-NEG-475-25-7D	Liver tissue	25GY	A
SA381560	20220917-NEG-477-25-7D	Liver tissue	25GY	A
SA381561	20220917-POS-403-25-7D	Liver tissue	25GY	A
SA381562	20220917-NEG-418-25-7D	Liver tissue	25GY	A
SA381563	20220708-POS-475-25-7D	Liver tissue	25GY	C8
SA381564	20220708-POS-477-25-7D	Liver tissue	25GY	C8
SA381565	20220708-POS-451-25-7D	Liver tissue	25GY	C8
SA381566	20220708-POS-444-25-7D	Liver tissue	25GY	C8
SA381567	20220708-POS-442-25-7D	Liver tissue	25GY	C8
SA381568	20220708-POS-418-25-7D	Liver tissue	25GY	C8
SA381569	20220708-POS-412-25-7D	Liver tissue	25GY	C8
SA381570	20220708-POS-403-25-7D	Liver tissue	25GY	C8
SA381571	20220808-444-25-7D	Liver tissue	25GY	GC
SA381572	20220808-418-25-7D	Liver tissue	25GY	GC
SA381573	20220808-403-25-7D	Liver tissue	25GY	GC
SA381574	20220808-442-25-7D	Liver tissue	25GY	GC
SA381575	20220808-412-25-7D	Liver tissue	25GY	GC
SA381576	20220808-451-25-7D	Liver tissue	25GY	GC
SA381577	20220808-475-25-7D	Liver tissue	25GY	GC
SA381578	20220808-477-25-7D	Liver tissue	25GY	GC
SA381579	20220712-NEG-412-25-7D	Liver tissue	25GY	T3
SA381580	20220712-NEG-418-25-7D	Liver tissue	25GY	T3
SA381581	20220712-NEG-442-25-7D	Liver tissue	25GY	T3
SA381582	20220712-NEG-444-25-7D	Liver tissue	25GY	T3
SA381583	20220712-NEG-451-25-7D	Liver tissue	25GY	T3
SA381584	20220712-NEG-477-25-7D	Liver tissue	25GY	T3
SA381585	20220712-NEG-403-25-7D	Liver tissue	25GY	T3
SA381586	20220712-NEG-475-25-7D	Liver tissue	25GY	T3
SA381587	20220917-POS-467-40-7D	Liver tissue	40GY	A
SA381588	20220917-POS-424-40-7D	Liver tissue	40GY	A
SA381589	20220917-POS-427-40-7D	Liver tissue	40GY	A
SA381590	20220917-POS-428-40-7D	Liver tissue	40GY	A
SA381591	20220917-POS-429-40-7D	Liver tissue	40GY	A
SA381592	20220917-POS-432-40-7D	Liver tissue	40GY	A
SA381593	20220917-NEG-428-40-7D	Liver tissue	40GY	A
SA381594	20220917-NEG-402-40-7D	Liver tissue	40GY	A
SA381595	20220917-NEG-419-40-7D	Liver tissue	40GY	A
SA381596	20220917-NEG-424-40-7D	Liver tissue	40GY	A
SA381597	20220917-NEG-427-40-7D	Liver tissue	40GY	A
SA381598	20220917-NEG-429-40-7D	Liver tissue	40GY	A
SA381599	20220917-NEG-432-40-7D	Liver tissue	40GY	A
SA381600	20220917-NEG-467-40-7D	Liver tissue	40GY	A
SA381601	20220917-POS-419-40-7D	Liver tissue	40GY	A
SA381602	20220917-POS-402-40-7D	Liver tissue	40GY	A
SA381603	20220708-POS-424-40-7D	Liver tissue	40GY	C8
SA381604	20220708-POS-467-40-7D	Liver tissue	40GY	C8
SA381605	20220708-POS-432-40-7D	Liver tissue	40GY	C8
SA381606	20220708-POS-429-40-7D	Liver tissue	40GY	C8
SA381607	20220708-POS-428-40-7D	Liver tissue	40GY	C8
SA381608	20220708-POS-427-40-7D	Liver tissue	40GY	C8
SA381609	20220708-POS-402-40-7D	Liver tissue	40GY	C8
SA381610	20220708-POS-419-40-7D	Liver tissue	40GY	C8
SA381611	20220808-467-40-7D	Liver tissue	40GY	GC
SA381612	20220808-427-40-7D	Liver tissue	40GY	GC
SA381613	20220808-424-40-7D	Liver tissue	40GY	GC
SA381614	20220808-428-40-7D	Liver tissue	40GY	GC
SA381615	20220808-429-40-7D	Liver tissue	40GY	GC
SA381616	20220808-432-40-7D	Liver tissue	40GY	GC
SA381617	20220808-419-40-7D	Liver tissue	40GY	GC
SA381618	20220808-402-40-7D	Liver tissue	40GY	GC
SA381619	20220712-NEG-467-40-7D	Liver tissue	40GY	T3
SA381620	20220712-NEG-432-40-7D	Liver tissue	40GY	T3
SA381621	20220712-NEG-429-40-7D	Liver tissue	40GY	T3
SA381622	20220712-NEG-427-40-7D	Liver tissue	40GY	T3
SA381623	20220712-NEG-424-40-7D	Liver tissue	40GY	T3
SA381624	20220712-NEG-419-40-7D	Liver tissue	40GY	T3
SA381625	20220712-NEG-402-40-7D	Liver tissue	40GY	T3
SA381626	20220712-NEG-428-40-7D	Liver tissue	40GY	T3
SA381627	20220917-NEG-453-C-7D	Liver tissue	Control	A
SA381628	20220917-NEG-478-C-7D	Liver tissue	Control	A
SA381629	20220917-NEG-472-C-7D	Liver tissue	Control	A
SA381630	20220917-NEG-448-C-7D	Liver tissue	Control	A
SA381631	20220917-NEG-435-C-7D	Liver tissue	Control	A
SA381632	20220917-NEG-433-C-7D	Liver tissue	Control	A
SA381633	20220917-NEG-416-C-7D	Liver tissue	Control	A
SA381634	20220917-NEG-410-C-7D	Liver tissue	Control	A
SA381635	20220917-POS-410-C-7D	Liver tissue	Control	A
SA381636	20220917-POS-433-C-7D	Liver tissue	Control	A
SA381637	20220917-POS-435-C-7D	Liver tissue	Control	A
SA381638	20220917-POS-448-C-7D	Liver tissue	Control	A
SA381639	20220917-POS-453-C-7D	Liver tissue	Control	A
SA381640	20220917-POS-472-C-7D	Liver tissue	Control	A
SA381641	20220917-POS-478-C-7D	Liver tissue	Control	A
SA381642	20220917-POS-416-C-7D	Liver tissue	Control	A
SA381643	20220708-POS-416-C-7D	Liver tissue	Control	C8
SA381644	20220708-POS-410-C-7D	Liver tissue	Control	C8
SA381645	20220708-POS-478-C-7D	Liver tissue	Control	C8
SA381646	20220708-POS-433-C-7D	Liver tissue	Control	C8

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Collection:

Collection ID:	CO003574
Collection Summary:	Male Sprague-Dawley (SD) rats (160–180 g) were obtained from the Shanghai SLAC Laboratory Animal Ltd (China), which were randomized into control (n=8) and irradiated cohorts (n=16). The experimental group was further subdivided into two irradiation dose groups: a low-dose irradiation group (25 Gy, n=8) and a high-dose irradiation group (40 Gy, n=8).Plasma was obtained through periorbital bleeding at time points of 3, 5 and 7 days post-irradiation, while liver tissue was collected at seventh day post-irradiation.
Sample Type:	blood（plasma）/liver tissue

Treatment:

Treatment ID:	TR003590
Treatment Summary:	After anesthetized with sufficient isoflurane in the gas anesthesia machine, the rats in the experimental groups were placed in a small animal radiotherapy treatment plan (X-RAD SmART) system. Images acquired through cone beam computed tomography (CT) were used to reconstruct and delineate targets. Multi-beam and CT guided Monte Carlo-based plans were performed to optimize doses to targets. The irradiation field encompassed the entire liver tissue, with an area of approximately 20×20mm. Each experimental group received a single dose of X-rays at 25 Gy or 40 Gy, respectively, with a dose rate of 2.98 Gy/min. In addition, the control group also underwent the same anesthesia procedure without irradiation.

Treatment ID:

TR003590

Treatment Summary:

After anesthetized with sufficient isoflurane in the gas anesthesia machine, the rats in the experimental groups were placed in a small animal radiotherapy treatment plan (X-RAD SmART) system. Images acquired through cone beam computed tomography (CT) were used to reconstruct and delineate targets. Multi-beam and CT guided Monte Carlo-based plans were performed to optimize doses to targets. The irradiation field encompassed the entire liver tissue, with an area of approximately 20×20mm. Each experimental group received a single dose of X-rays at 25 Gy or 40 Gy, respectively, with a dose rate of 2.98 Gy/min. In addition, the control group also underwent the same anesthesia procedure without irradiation.

Sample Preparation:

Sampleprep ID:	SP003588
Sampleprep Summary:	LC-MS：For liver tissue, about 20mg samples were homogenized with ceramic beads in water (300μL) using a Tissue Lyser homogenizer (Gene Ready Ultracool, Life Real, China). The homogenization took 5 min with 15 s intervals each time (45 HZ), then 600μL acetonitrile containing ISs (Table S ) and 600μL methanol were added followed by vortex for 1 min at 4–8°C. After ultrasonic treatment in an ice bath for 10 minutes, placing in a -20℃ refrigerator for 1 hour, and then two aliquots of supernatant with each 600μL were collected by centrifugation at 13000rpm for 15 min at 4°C. Finally, the liquid supernatant was freeze-dried and stored at -80℃. Similarly, 200 μL ISs was added into 50 μL plasma for the protein precipitation. After vortexing, the sample was centrifuged at 13,000 rpm/min for 10 min (4℃), the supernatant was taken and divided into two parts, followed lyophilized by vacuum and stored at -80℃. The composition and concentration of internal standards (ISs) for liver tissues and plasma samples were listed in Table S1 and S2. GC-MS：For liver tissue preparation for GC-MS, The extraction process of metabolites including the lyophilized procedure for the liver samples is same as that of for LC-MS. After that, the lyophilized liver samples was resolved in 50 µL methoxyamine solution (20mg/ml) and vortexed for 1 min. Then, the sample was placed in 37°C metal bath for 1.5 h oximation reaction followed by silylation reaction with 40 μL of MSTFA in 37°C metal bath for 1 h. After derivatization, the solution was centrifuged (13000 rpm for 15 min at 4°C) and the supernatant was collected for the GC–MS analysis. For plasma sample, 50 μL of plasma was added 200μL methanol containing the ISs (Table S) and vortexed for 1min. The solution was centrifuged at 1300,000 rpm for 15 min at 4°C. Then, the supernatant solution was collected and lyophilized. Subsequently, the residue was conducted a two-step derivatization, similar to the liver tissue mentioned above.

Sampleprep ID:

SP003588

Sampleprep Summary:

LC-MS：For liver tissue, about 20mg samples were homogenized with ceramic beads in water (300μL) using a Tissue Lyser homogenizer (Gene Ready Ultracool, Life Real, China). The homogenization took 5 min with 15 s intervals each time (45 HZ), then 600μL acetonitrile containing ISs (Table S ) and 600μL methanol were added followed by vortex for 1 min at 4–8°C. After ultrasonic treatment in an ice bath for 10 minutes, placing in a -20℃ refrigerator for 1 hour, and then two aliquots of supernatant with each 600μL were collected by centrifugation at 13000rpm for 15 min at 4°C. Finally, the liquid supernatant was freeze-dried and stored at -80℃. Similarly, 200 μL ISs was added into 50 μL plasma for the protein precipitation. After vortexing, the sample was centrifuged at 13,000 rpm/min for 10 min (4℃), the supernatant was taken and divided into two parts, followed lyophilized by vacuum and stored at -80℃. The composition and concentration of internal standards (ISs) for liver tissues and plasma samples were listed in Table S1 and S2. GC-MS：For liver tissue preparation for GC-MS, The extraction process of metabolites including the lyophilized procedure for the liver samples is same as that of for LC-MS. After that, the lyophilized liver samples was resolved in 50 µL methoxyamine solution (20mg/ml) and vortexed for 1 min. Then, the sample was placed in 37°C metal bath for 1.5 h oximation reaction followed by silylation reaction with 40 μL of MSTFA in 37°C metal bath for 1 h. After derivatization, the solution was centrifuged (13000 rpm for 15 min at 4°C) and the supernatant was collected for the GC–MS analysis. For plasma sample, 50 μL of plasma was added 200μL methanol containing the ISs (Table S) and vortexed for 1min. The solution was centrifuged at 1300,000 rpm for 15 min at 4°C. Then, the supernatant solution was collected and lyophilized. Subsequently, the residue was conducted a two-step derivatization, similar to the liver tissue mentioned above.

Combined analysis:

Analysis ID	AN005672	AN005673	AN005674
Analysis type	MS	MS	MS
Chromatography type	Reverse Phase	Normal phase	GC
Chromatography system	Thermo TSQ Vantage (HPLC-MS/MS）	Thermo TSQ Vantage (HPLC-MS/MS）	Shimadzu GC-2010
Column	Waters ACQUITY UPLC HSS T3（100 x 2.1mm，1.8um）	Waters ACQUITY UPLC BEH C8（100 x 2.1mm，1.7um）	Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type	ESI	ESI	EI
MS instrument type	Triple quadrupole	Triple quadrupole	Triple quadrupole
MS instrument name	Thermo TSQ Vantage	Thermo TSQ Vantage	Shimadzu QP2010 Plus
Ion Mode	NEGATIVE	POSITIVE	POSITIVE
Units	peak area	peak area	peak area

Chromatography:

Chromatography ID:	CH004307
Chromatography Summary:	Negative ion mode
Instrument Name:	Thermo TSQ Vantage (HPLC-MS/MS）
Column Name:	Waters ACQUITY UPLC HSS T3（100 x 2.1mm，1.8um）
Column Temperature:	55°C
Flow Gradient:	0~1 min, 2% B; 1-20 min, 2~100% B; 20~24min, 100% B; 24~24.5min, 100~2% B; 24.5~34 min, 2% B
Flow Rate:	0.35 mL/min
Solvent A:	100% water; 0.1% formic acid
Solvent B:	100% acetonitrile; 0.1% formic acid
Chromatography Type:	Reverse Phase

Chromatography ID:	CH004308
Chromatography Summary:	positive ion mode
Instrument Name:	Thermo TSQ Vantage (HPLC-MS/MS）
Column Name:	Waters ACQUITY UPLC BEH C8（100 x 2.1mm，1.7um）
Column Temperature:	50°C
Flow Gradient:	0-0.5min, 5% B; 0.5-24min, 5-100% B; 24-28 min, 40-100% B; 28-28.5min, 100-5% B; 28.5-48 min, 5% B
Flow Rate:	0.35 mL/min
Solvent A:	water(0.1% formic acid )
Solvent B:	acetonitrile(0.1% formic acid )
Chromatography Type:	Normal phase

Chromatography ID:	CH004309
Chromatography Summary:	GC
Instrument Name:	Shimadzu GC-2010
Column Name:	Agilent DB5-MS (30m x 0.25mm, 0.25um)
Column Temperature:	70°C
Flow Gradient:	N/A
Flow Rate:	1.2 mL/min
Solvent A:	N/A
Solvent B:	N/A
Chromatography Type:	GC

MS:

MS ID:	MS005396
Analysis ID:	AN005672
Instrument Name:	Thermo TSQ Vantage
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	The temperature of ion source and ion transport tube is 350℃, the electrospray voltage in positive and negative ion mode is -2,500 V respectively, the sheath pressure is 35 Arb, and the auxiliary pressure is 10 Arb. Data acquisition and pre-processing and instrument interface control are performed in Xcalibur (Thermo, USA) software.
Ion Mode:	NEGATIVE

MS ID:	MS005397
Analysis ID:	AN005673
Instrument Name:	Thermo TSQ Vantage
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	The temperature of ion source and ion transport tube is 350℃, the electrospray voltage in positive and negative ion mode is 3,000 V respectively, the sheath pressure is 35 Arb, and the auxiliary pressure is 10 Arb. Data acquisition and pre-processing and instrument interface control are performed in Xcalibur (Thermo, USA) software.
Ion Mode:	POSITIVE

MS ID:	MS005398
Analysis ID:	AN005674
Instrument Name:	Shimadzu QP2010 Plus
Instrument Type:	Triple quadrupole
MS Type:	EI
MS Comments:	GC-MS metabolic analysis was performed with Shimadzu QP2010 GC-MS system equipped with AOC 20i auto-injector (Shimadzu, Japan). 1 mL was injected in split mode (ratio 20 : 1) and chromatographic separation was achieved on a DB-5MS column (0.25 mm, 0.25 mm 30 m, J&W Scientific, USA), helium carrier gas was operated at constant flow rate 1.2 mL/ min, and the GC oven temperature program was started initially at 70°C, held for 3 min, increased to 310°C at 5℃/min and kept for 10 min. The inlet temperature was 300°C. Helium (99.9995%, sourced from China) served as the carrier gas, maintained at a constant linear velocity of 40 cm/s. An electron ionization (EI) source was employed, with an ionization voltage set at 70 eV. The detection voltage was adjusted based on the autotuning results. Data acquisition commenced at 5.7 minutes, and the mass scan range was set between 33 and 600 m/z. The temperatures of the transfer line and the ion source were maintained at 280°C and 230°C, respectively.
Ion Mode:	POSITIVE