Summary of Study ST004170

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 PR002630. The data can be accessed directly via it's Project DOI: 10.21228/M8PV7C This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST004170
Study Title	Untargeted Metabolomics for Assessing Neural Stem Cell Therapy in Spinal Cord Injury
Study Summary	To investigate the metabolic regulatory role of neural stem cell transplantation in spinal cord injury, this study established a rat spinal cord injury model and implanted collagen-based materials loaded with or without neural stem cells into the lesion site. Three days post injury, we collected spinal cord tissue from the lesion site and performed untargeted metabolomic analysis. The experiment was divided into four groups: sham operation group, spinal cord injury model group, material-only control group, and neural stem cell-loaded material group.Using LC-MS analysis, we identified 137 reference matched metabolites in positive ion mode and 121 reference matched metabolites in negative ion mode. Bioinformatics analysis revealed 15 metabolites that were highly expressed in the NSC transplantation group, including neurotransmitter (5-hydroxyindoleacetic acid), fatty acids and derivatives (palmitic acid, stearic acid, linoleic acid, Acar17:0), sphingolipid (sphingosine), lysophosphatidylcholines (LPC15:0, LPC17:0, LPC18:0, LPC22:5), endocannabinoids (arachidonoyl ethanolamine), and others. Our findings highlight the pivotal regulatory role of NSC-derived metabolites in post-injury microenvironment, offering novel mechanistic insights into metabolic reprogramming for SCI recovery via cell-based therapeutics.
Institute	Nanjing University
Department	Clinical Stem Cell Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, 210009, China
Last Name	Chen
First Name	Dong
Address	358 ZhongShan Rd.
Email	chendongqub@126.com
Phone	17372774161
Submit Date	2025-09-01
Raw Data Available	Yes
Raw Data File Type(s)	mzXML, wiff
Analysis Type Detail	LC-MS
Release Date	2025-09-09
Release Version	1

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Project:

Project ID:	PR002630
Project DOI:	doi: 10.21228/M8PV7C
Project Title:	Untargeted Metabolomics for Assessing Neural Stem Cell Therapy in Spinal Cord Injury
Project Type:	LC-MS untargeted metabolomics
Project Summary:	Spinal cord injury remains a devastating condition with limited therapeutic options. Neural stem cell therapy for spinal cord injury represents a novel therapeutic strategy; however, the underlying mechanisms require further investigation. This study utilized an untargeted metabolomics approach to explore the effects of in situ neural stem cell transplantation on the metabolic microenvironment of spinal cord tissue after injury. We aim to identify key metabolic molecules involved in neural stem cell transplantation for spinal cord injury through metabolomics approaches, thereby providing a theoretical foundation for subsequent clinical translation.
Institute:	Nanjing University
Department:	Clinical Stem Cell Center, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, 210009, China
Last Name:	Chen
First Name:	Dong
Address:	358 ZhongShan Rd., Nanjing, JiangSu, 210009, China
Email:	chendongqub@126.com
Phone:	+86 17372774161

Subject:

Subject ID:	SU004321
Subject Type:	Mammal
Subject Species:	Rattus norvegicus
Taxonomy ID:	10116
Weight Or Weight Range:	220-250g/rat
Gender:	Female
Animal Animal Supplier:	the Laboratory Animal Center of Nanjing Medical University
Animal Housing:	the Laboratory Animal Center of Nanjing Drum Tower Hospital
Animal Light Cycle:	12-hour light/dark cycle
Animal Feed:	free access to normal diet and water

Factors:

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

mb_sample_id	local_sample_id	Sample source	Injection order	Treatment
SA481708	POS_QC_08	pooled quality control	15	NA
SA481709	POS_QC_06	pooled quality control	1	NA
SA481710	POS_QC_09	pooled quality control	21	NA
SA481711	POS_QC_10	pooled quality control	28	NA
SA481712	POS_QC_11	pooled quality control	35	NA
SA481713	POS_QC_12	pooled quality control	41	NA
SA481714	POS_QC_13	pooled quality control	44	NA
SA481715	NEG_QC_06	pooled quality control	45	NA
SA481716	NEG_QC_07	pooled quality control	52	NA
SA481717	NEG_QC_08	pooled quality control	59	NA
SA481718	NEG_QC_09	pooled quality control	65	NA
SA481719	NEG_QC_10	pooled quality control	72	NA
SA481720	NEG_QC_11	pooled quality control	79	NA
SA481721	NEG_QC_12	pooled quality control	85	NA
SA481722	NEG_QC_13	pooled quality control	88	NA
SA481723	POS_QC_07	pooled quality control	8	NA
SA481724	POS_M763	spinal cord tissue	10	spinal cord injury model (SCI model)
SA481725	POS_M764	spinal cord tissue	11	spinal cord injury model (SCI model)
SA481726	POS_S713	spinal cord tissue	12	sham (laminectomy only)
SA481727	POS_S741	spinal cord tissue	13	sham (laminectomy only)
SA481728	POS_N754	spinal cord tissue	14	neural stem cell loaded scaffold transplantation
SA481729	POS_N761	spinal cord tissue	16	neural stem cell loaded scaffold transplantation
SA481730	POS_M707	spinal cord tissue	17	spinal cord injury model (SCI model)
SA481731	POS_M706	spinal cord tissue	18	spinal cord injury model (SCI model)
SA481732	POS_S742	spinal cord tissue	19	sham (laminectomy only)
SA481733	POS_C726	spinal cord tissue	20	scaffold-only transplantation
SA481734	POS_S738	spinal cord tissue	22	sham (laminectomy only)
SA481735	POS_S737	spinal cord tissue	23	sham (laminectomy only)
SA481736	POS_S740	spinal cord tissue	24	sham (laminectomy only)
SA481737	POS_C729	spinal cord tissue	25	scaffold-only transplantation
SA481738	POS_C727	spinal cord tissue	26	scaffold-only transplantation
SA481739	POS_M701	spinal cord tissue	27	spinal cord injury model (SCI model)
SA481740	POS_C725	spinal cord tissue	29	scaffold-only transplantation
SA481741	POS_N705	spinal cord tissue	2	neural stem cell loaded scaffold transplantation
SA481742	POS_S739	spinal cord tissue	30	sham (laminectomy only)
SA481743	POS_N759	spinal cord tissue	31	neural stem cell loaded scaffold transplantation
SA481744	POS_M753	spinal cord tissue	32	spinal cord injury model (SCI model)
SA481745	POS_N757	spinal cord tissue	33	neural stem cell loaded scaffold transplantation
SA481746	POS_N756	spinal cord tissue	34	neural stem cell loaded scaffold transplantation
SA481747	POS_N755	spinal cord tissue	36	neural stem cell loaded scaffold transplantation
SA481748	POS_C711	spinal cord tissue	37	scaffold-only transplantation
SA481749	POS_C710	spinal cord tissue	38	scaffold-only transplantation
SA481750	POS_C709	spinal cord tissue	39	scaffold-only transplantation
SA481751	POS_C712	spinal cord tissue	3	scaffold-only transplantation
SA481752	POS_M708	spinal cord tissue	40	spinal cord injury model (SCI model)
SA481753	POS_M758	spinal cord tissue	42	spinal cord injury model (SCI model)
SA481754	POS_M762	spinal cord tissue	43	spinal cord injury model (SCI model)
SA481755	NEG_N705	spinal cord tissue	46	neural stem cell loaded scaffold transplantation
SA481756	NEG_C712	spinal cord tissue	47	scaffold-only transplantation
SA481757	NEG_N704	spinal cord tissue	48	neural stem cell loaded scaffold transplantation
SA481758	NEG_N703	spinal cord tissue	49	scaffold-only transplantation
SA481759	POS_N704	spinal cord tissue	4	neural stem cell loaded scaffold transplantation
SA481760	NEG_S715	spinal cord tissue	50	sham (laminectomy only)
SA481761	NEG_S714	spinal cord tissue	51	sham (laminectomy only)
SA481762	NEG_M728	spinal cord tissue	53	spinal cord injury model (SCI model)
SA481763	NEG_M763	spinal cord tissue	54	spinal cord injury model (SCI model)
SA481764	NEG_M764	spinal cord tissue	55	spinal cord injury model (SCI model)
SA481765	NEG_S713	spinal cord tissue	56	sham (laminectomy only)
SA481766	NEG_S741	spinal cord tissue	57	sham (laminectomy only)
SA481767	NEG_N754	spinal cord tissue	58	neural stem cell loaded scaffold transplantation
SA481768	POS_N703	spinal cord tissue	5	scaffold-only transplantation
SA481769	NEG_N761	spinal cord tissue	60	neural stem cell loaded scaffold transplantation
SA481770	NEG_M707	spinal cord tissue	61	spinal cord injury model (SCI model)
SA481771	NEG_M706	spinal cord tissue	62	spinal cord injury model (SCI model)
SA481772	NEG_S742	spinal cord tissue	63	sham (laminectomy only)
SA481773	NEG_C726	spinal cord tissue	64	scaffold-only transplantation
SA481774	NEG_S738	spinal cord tissue	66	sham (laminectomy only)
SA481775	NEG_S737	spinal cord tissue	67	sham (laminectomy only)
SA481776	NEG_S740	spinal cord tissue	68	sham (laminectomy only)
SA481777	NEG_C729	spinal cord tissue	69	scaffold-only transplantation
SA481778	POS_S715	spinal cord tissue	6	sham (laminectomy only)
SA481779	NEG_C727	spinal cord tissue	70	scaffold-only transplantation
SA481780	NEG_M701	spinal cord tissue	71	spinal cord injury model (SCI model)
SA481781	NEG_C725	spinal cord tissue	73	scaffold-only transplantation
SA481782	NEG_S739	spinal cord tissue	74	sham (laminectomy only)
SA481783	NEG_N759	spinal cord tissue	75	neural stem cell loaded scaffold transplantation
SA481784	NEG_M753	spinal cord tissue	76	spinal cord injury model (SCI model)
SA481785	NEG_N757	spinal cord tissue	77	neural stem cell loaded scaffold transplantation
SA481786	NEG_N756	spinal cord tissue	78	neural stem cell loaded scaffold transplantation
SA481787	POS_S714	spinal cord tissue	7	sham (laminectomy only)
SA481788	NEG_N755	spinal cord tissue	80	neural stem cell loaded scaffold transplantation
SA481789	NEG_C711	spinal cord tissue	81	scaffold-only transplantation
SA481790	NEG_C710	spinal cord tissue	82	scaffold-only transplantation
SA481791	NEG_C709	spinal cord tissue	83	scaffold-only transplantation
SA481792	NEG_M708	spinal cord tissue	84	spinal cord injury model (SCI model)
SA481793	NEG_M758	spinal cord tissue	86	spinal cord injury model (SCI model)
SA481794	NEG_M762	spinal cord tissue	87	spinal cord injury model (SCI model)
SA481795	POS_M728	spinal cord tissue	9	spinal cord injury model (SCI model)

Showing results 1 to 88 of 88

Showing results 1 to 88 of 88

Collection:

Collection ID:	CO004314
Collection Summary:	This study investigates the metabolic regulatory effects of neural stem cell transplantation in spinal cord injury (SCI). The rat SCI model was established as below: A laminectomy was performed at vertebral levels T7-T9 to expose the spinal cord. Then a 3-mm long segment of spinal cord tissue was completely transected. Sham-operated rats received a laminectomy only. For cell transplantation, NSCs (1 × 10^6 cells in 20 μL of normal saline) were loaded into a pre-sterilized multi-channel collagen scaffold (3 × 3 × 3 mm) and engrafted to the cavity at the injury site. Three days after spinal cord injury, the rats were sacrificed and dissected. Approximately 2 cm of tissue surrounding the injury site was collected, rapidly frozen in liquid nitrogen, and stored at -80°C. After the collection of all experimental tissues, the collected spinal cord tissues were cut and weighed, with each sample approximately 50 mg, and placed in 2 ml centrifuge tubes stored on ice awaiting further pre-processing.
Sample Type:	Spinal cord
Storage Conditions:	-80℃

Treatment:

Treatment ID:	TR004330
Treatment Summary:	A laminectomy was performed at vertebral levels T7-T9 to expose the spinal cord. Then a 3-mm long segment of spinal cord tissue was completely transected. Sham-operated rats received a laminectomy only. For cell transplantation, neural stem cells (1 × 10^6 cells in 20 μL of normal saline) were loaded into a pre-sterilized multi-channel collagen scaffold (3 × 3 × 3 mm) and engrafted to the cavity at the injury site.
Treatment:	cell transplantation
Treatment Compound:	neural stem cells (NSCs)
Treatment Route:	In situ transplantation
Treatment Dose:	1 × 10^6 cells in 20 μL of normal saline per rat
Treatment Dosevolume:	1 × 10^6 cells in 20 μL of normal saline per rat
Treatment Doseduration:	1 × 10^6 cells in 20 μL of normal saline per rat
Treatment Vehicle:	normal saline
Animal Anesthesia:	Isoflurane

Sample Preparation:

Sampleprep ID:	SP004327
Sampleprep Summary:	Approximately 50 mg of each spinal cord tissue sample was weighed and homogenized in ice-cold 80% methanol (1:20, tissue weight (mg): solvent volume (μL)) using a tissue grinder. Homogenates were incubated at -40 °C for 4 hours and subsequently centrifugated at 13000 × g for 20 minutes at 4°C. The supernatant was collected, dried using a centrifugal concentrator, and stored at -80 °C. Prior to metabolomic analysis, all dried samples were redissolved and processed identically. A (QC) sample from all spinal cord samples was prepared for monitoring the stability of the analysis.

Sampleprep ID:

SP004327

Sampleprep Summary:

Approximately 50 mg of each spinal cord tissue sample was weighed and homogenized in ice-cold 80% methanol (1:20, tissue weight (mg): solvent volume (μL)) using a tissue grinder. Homogenates were incubated at -40 °C for 4 hours and subsequently centrifugated at 13000 × g for 20 minutes at 4°C. The supernatant was collected, dried using a centrifugal concentrator, and stored at -80 °C. Prior to metabolomic analysis, all dried samples were redissolved and processed identically. A (QC) sample from all spinal cord samples was prepared for monitoring the stability of the analysis.

Combined analysis:

Analysis ID	AN006922	AN006923
Chromatography ID	CH005257	CH005257
MS ID	MS006619	MS006620
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Shimadzu ExionLC system	Shimadzu ExionLC system
Column	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
MS Type	ESI	ESI
MS instrument type	Triple TOF	Triple TOF
MS instrument name	ABI Sciex 5600+ TripleTOF	ABI Sciex 5600+ TripleTOF
Ion Mode	POSITIVE	NEGATIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH005257
Chromatography Summary:	Chromatographic Separation: Liquid chromatography was performed using a Shimadzu ExionLC system equipped with a Waters ACQUITY HSS T3 column (2.1 × 100 mm, 1.8 μm). The mobile phase consisted of (A) 0.1% formic acid in water and (B) 0.1% formic acid in acetonitrile. The optimized ultra-high-performance liquid chromatography (UHPLC) gradient elution program was as follows: 0–1.5 min, 99.0% B; 1.5–13.0 min, 99.0% to 1.0% B; 13.0–16.5 min, 1.0% B; 16.5–20.0 min, 99.0% B. The flow rate was maintained at 0.30 ml/min, and the column temperature was set at 40°C. A 2 μl aliquot of each sample was injected per run. Samples were analyzed in a random order, with a pooled QC sample inserted after every six test samples.
Instrument Name:	Shimadzu ExionLC system
Column Name:	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:	40°C
Flow Gradient:	0–1.5 min, 99.0% B; 1.5–13.0 min, 99.0% to 1.0% B; 13.0–16.5 min, 1.0% B; 16.5–16.6 min, 1.0% to 99% B, 16.6-20.0 min, 99.0% B.
Flow Rate:	0.30 mL/min
Solvent A:	100% Water; 0.1% formic acid
Solvent B:	100% Acetonitrile; 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS006619
Analysis ID:	AN006922
Instrument Name:	ABI Sciex 5600+ TripleTOF
Instrument Type:	Triple TOF
MS Type:	ESI
MS Comments:	The full scan covered a mass range from m/z 50 to 1000 Da. Ion spray voltages of +5500V for positive ion mode and -4500V for negative ion mode. Nitrogen was used as the nebulizer, heater and curtain gas at constant flow rates of 55, 55 and 35 psi, respectively. MS/MS data was acquired using an information-dependent acquisition approach in high-sensitivity mode and real-time dynamic background subtraction. Collision was set at 35eV with a spread of 10eV. Mass calibration was automatically performed by the calibrant delivery system, which infused the atmospheric pressure chemical ionization (APCI) calibration solution every 5 samples.
Ion Mode:	POSITIVE

MS ID:	MS006620
Analysis ID:	AN006923
Instrument Name:	ABI Sciex 5600+ TripleTOF
Instrument Type:	Triple TOF
MS Type:	ESI
MS Comments:	The full scan covered a mass range from m/z 50 to 1000 Da. Ion spray voltages of +5500V for positive ion mode and -4500V for negative ion mode. Nitrogen was used as the nebulizer, heater and curtain gas at constant flow rates of 55, 55 and 35 psi, respectively. MS/MS data was acquired using an information-dependent acquisition approach in high-sensitivity mode and real-time dynamic background subtraction. Collision was set at 35eV with a spread of 10eV. Mass calibration was automatically performed by the calibrant delivery system, which infused the atmospheric pressure chemical ionization (APCI) calibration solution every 5 samples.
Ion Mode:	NEGATIVE