#METABOLOMICS WORKBENCH chendongqub_20250901_200021 DATATRACK_ID:6361 STUDY_ID:ST004170 ANALYSIS_ID:AN006922 PROJECT_ID:PR002630
VERSION                          	1
CREATED_ON                       	10-21-2025
#PROJECT
PR:PROJECT_TITLE                 	Untargeted Metabolomics for Assessing Neural Stem Cell Therapy in Spinal Cord
PR:PROJECT_TITLE                 	Injury
PR:PROJECT_TYPE                  	LC-MS untargeted metabolomics
PR:PROJECT_SUMMARY               	Spinal cord injury remains a devastating condition with limited therapeutic
PR:PROJECT_SUMMARY               	options. Neural stem cell therapy for spinal cord injury represents a novel
PR:PROJECT_SUMMARY               	therapeutic strategy; however, the underlying mechanisms require further
PR:PROJECT_SUMMARY               	investigation. This study utilized an untargeted metabolomics approach to
PR:PROJECT_SUMMARY               	explore the effects of in situ neural stem cell transplantation on the metabolic
PR:PROJECT_SUMMARY               	microenvironment of spinal cord tissue after injury. We aim to identify key
PR:PROJECT_SUMMARY               	metabolic molecules involved in neural stem cell transplantation for spinal cord
PR:PROJECT_SUMMARY               	injury through metabolomics approaches, thereby providing a theoretical
PR:PROJECT_SUMMARY               	foundation for subsequent clinical translation.
PR:INSTITUTE                     	Nanjing University
PR:DEPARTMENT                    	Clinical Stem Cell Center, Nanjing Drum Tower Hospital, Affiliated Hospital of
PR:DEPARTMENT                    	Medical School, Nanjing University, Nanjing, Jiangsu Province, 210009, China
PR:LAST_NAME                     	Chen
PR:FIRST_NAME                    	Dong
PR:ADDRESS                       	358 ZhongShan Rd., Nanjing, JiangSu, 210009, China
PR:EMAIL                         	chendongqub@126.com
PR:PHONE                         	+86 17372774161
PR:DOI                           	http://dx.doi.org/10.21228/M8PV7C
#STUDY
ST:STUDY_TITLE                   	Untargeted Metabolomics for Assessing Neural Stem Cell Therapy in Spinal Cord
ST:STUDY_TITLE                   	Injury
ST:STUDY_SUMMARY                 	To investigate the metabolic regulatory role of neural stem cell transplantation
ST:STUDY_SUMMARY                 	in spinal cord injury, this study established a rat spinal cord injury model and
ST:STUDY_SUMMARY                 	implanted collagen-based materials loaded with or without neural stem cells into
ST:STUDY_SUMMARY                 	the lesion site. Three days post injury, we collected spinal cord tissue from
ST:STUDY_SUMMARY                 	the lesion site and performed untargeted metabolomic analysis. The experiment
ST:STUDY_SUMMARY                 	was divided into four groups: sham operation group, spinal cord injury model
ST:STUDY_SUMMARY                 	group, material-only control group, and neural stem cell-loaded material
ST:STUDY_SUMMARY                 	group.Using LC-MS analysis, we identified 137 reference matched metabolites in
ST:STUDY_SUMMARY                 	positive ion mode and 121 reference matched metabolites in negative ion mode.
ST:STUDY_SUMMARY                 	Bioinformatics analysis revealed 15 metabolites that were highly expressed in
ST:STUDY_SUMMARY                 	the NSC transplantation group, including neurotransmitter (5-hydroxyindoleacetic
ST:STUDY_SUMMARY                 	acid), fatty acids and derivatives (palmitic acid, stearic acid, linoleic acid,
ST:STUDY_SUMMARY                 	Acar17:0), sphingolipid (sphingosine), lysophosphatidylcholines (LPC15:0,
ST:STUDY_SUMMARY                 	LPC17:0, LPC18:0, LPC22:5), endocannabinoids (arachidonoyl ethanolamine), and
ST:STUDY_SUMMARY                 	others. Our findings highlight the pivotal regulatory role of NSC-derived
ST:STUDY_SUMMARY                 	metabolites in post-injury microenvironment, offering novel mechanistic insights
ST:STUDY_SUMMARY                 	into metabolic reprogramming for SCI recovery via cell-based therapeutics.
ST:INSTITUTE                     	Nanjing University
ST:DEPARTMENT                    	Clinical Stem Cell Center, Nanjing Drum Tower Hospital, Affiliated Hospital of
ST:DEPARTMENT                    	Medical School, Nanjing University, Nanjing, Jiangsu Province, 210009, China
ST:LAST_NAME                     	Chen
ST:FIRST_NAME                    	Dong
ST:ADDRESS                       	358 ZhongShan Rd.
ST:EMAIL                         	chendongqub@126.com
ST:PHONE                         	17372774161
ST:SUBMIT_DATE                   	2025-09-01
#SUBJECT
SU:SUBJECT_TYPE                  	Mammal
SU:SUBJECT_SPECIES               	Rattus norvegicus
SU:TAXONOMY_ID                   	10116
SU:WEIGHT_OR_WEIGHT_RANGE        	220-250g/rat
SU:GENDER                        	Female
SU:ANIMAL_ANIMAL_SUPPLIER        	the Laboratory Animal Center of Nanjing Medical University
SU:ANIMAL_HOUSING                	the Laboratory Animal Center of Nanjing Drum Tower Hospital
SU:ANIMAL_LIGHT_CYCLE            	12-hour light/dark cycle
SU:ANIMAL_FEED                   	free access to normal diet and water
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_08	Sample source:pooled quality control | Injection order:15 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_08.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_06	Sample source:pooled quality control | Injection order:1 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_06.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_09	Sample source:pooled quality control | Injection order:21 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_09.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_10	Sample source:pooled quality control | Injection order:28 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_10.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_11	Sample source:pooled quality control | Injection order:35 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_11.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_12	Sample source:pooled quality control | Injection order:41 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_12.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_13	Sample source:pooled quality control | Injection order:44 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_13.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_06	Sample source:pooled quality control | Injection order:45 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_06.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_07	Sample source:pooled quality control | Injection order:52 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_07.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_08	Sample source:pooled quality control | Injection order:59 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_08.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_09	Sample source:pooled quality control | Injection order:65 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_09.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_10	Sample source:pooled quality control | Injection order:72 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_10.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_11	Sample source:pooled quality control | Injection order:79 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_11.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_12	Sample source:pooled quality control | Injection order:85 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_12.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_QC_13	Sample source:pooled quality control | Injection order:88 | Treatment:NA	RAW_FILE_NAME(Raw file name)=NEG_QC_13.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_QC_07	Sample source:pooled quality control | Injection order:8 | Treatment:NA	RAW_FILE_NAME(Raw file name)=POS_QC_07.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M763	Sample source:spinal cord tissue | Injection order:10 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M763.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M764	Sample source:spinal cord tissue | Injection order:11 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M764.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S713	Sample source:spinal cord tissue | Injection order:12 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S713.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S741	Sample source:spinal cord tissue | Injection order:13 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S741.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N754	Sample source:spinal cord tissue | Injection order:14 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N754.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N761	Sample source:spinal cord tissue | Injection order:16 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N761.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M707	Sample source:spinal cord tissue | Injection order:17 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M707.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M706	Sample source:spinal cord tissue | Injection order:18 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M706.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S742	Sample source:spinal cord tissue | Injection order:19 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S742.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C726	Sample source:spinal cord tissue | Injection order:20 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C726.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S738	Sample source:spinal cord tissue | Injection order:22 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S738.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S737	Sample source:spinal cord tissue | Injection order:23 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S737.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S740	Sample source:spinal cord tissue | Injection order:24 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S740.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C729	Sample source:spinal cord tissue | Injection order:25 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C729.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C727	Sample source:spinal cord tissue | Injection order:26 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C727.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M701	Sample source:spinal cord tissue | Injection order:27 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M701.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C725	Sample source:spinal cord tissue | Injection order:29 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C725.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N705	Sample source:spinal cord tissue | Injection order:2 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N705.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S739	Sample source:spinal cord tissue | Injection order:30 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S739.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N759	Sample source:spinal cord tissue | Injection order:31 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N759.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M753	Sample source:spinal cord tissue | Injection order:32 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M753.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N757	Sample source:spinal cord tissue | Injection order:33 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N757.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N756	Sample source:spinal cord tissue | Injection order:34 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N756.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N755	Sample source:spinal cord tissue | Injection order:36 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N755.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C711	Sample source:spinal cord tissue | Injection order:37 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C711.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C710	Sample source:spinal cord tissue | Injection order:38 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C710.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C709	Sample source:spinal cord tissue | Injection order:39 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C709.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_C712	Sample source:spinal cord tissue | Injection order:3 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_C712.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M708	Sample source:spinal cord tissue | Injection order:40 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M708.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M758	Sample source:spinal cord tissue | Injection order:42 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M758.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M762	Sample source:spinal cord tissue | Injection order:43 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M762.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N705	Sample source:spinal cord tissue | Injection order:46 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N705.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C712	Sample source:spinal cord tissue | Injection order:47 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C712.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N704	Sample source:spinal cord tissue | Injection order:48 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N704.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N703	Sample source:spinal cord tissue | Injection order:49 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_N703.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N704	Sample source:spinal cord tissue | Injection order:4 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=POS_N704.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S715	Sample source:spinal cord tissue | Injection order:50 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S715.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S714	Sample source:spinal cord tissue | Injection order:51 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S714.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M728	Sample source:spinal cord tissue | Injection order:53 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M728.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M763	Sample source:spinal cord tissue | Injection order:54 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M763.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M764	Sample source:spinal cord tissue | Injection order:55 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M764.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S713	Sample source:spinal cord tissue | Injection order:56 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S713.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S741	Sample source:spinal cord tissue | Injection order:57 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S741.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N754	Sample source:spinal cord tissue | Injection order:58 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N754.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_N703	Sample source:spinal cord tissue | Injection order:5 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=POS_N703.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N761	Sample source:spinal cord tissue | Injection order:60 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N761.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M707	Sample source:spinal cord tissue | Injection order:61 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M707.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M706	Sample source:spinal cord tissue | Injection order:62 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M706.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S742	Sample source:spinal cord tissue | Injection order:63 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S742.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C726	Sample source:spinal cord tissue | Injection order:64 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C726.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S738	Sample source:spinal cord tissue | Injection order:66 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S738.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S737	Sample source:spinal cord tissue | Injection order:67 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S737.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S740	Sample source:spinal cord tissue | Injection order:68 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S740.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C729	Sample source:spinal cord tissue | Injection order:69 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C729.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S715	Sample source:spinal cord tissue | Injection order:6 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S715.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C727	Sample source:spinal cord tissue | Injection order:70 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C727.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M701	Sample source:spinal cord tissue | Injection order:71 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M701.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C725	Sample source:spinal cord tissue | Injection order:73 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C725.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_S739	Sample source:spinal cord tissue | Injection order:74 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=NEG_S739.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N759	Sample source:spinal cord tissue | Injection order:75 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N759.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M753	Sample source:spinal cord tissue | Injection order:76 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M753.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N757	Sample source:spinal cord tissue | Injection order:77 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N757.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N756	Sample source:spinal cord tissue | Injection order:78 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N756.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_S714	Sample source:spinal cord tissue | Injection order:7 | Treatment:sham (laminectomy only)	RAW_FILE_NAME(Raw file name)=POS_S714.wiff; ion mode=positive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_N755	Sample source:spinal cord tissue | Injection order:80 | Treatment:neural stem cell loaded scaffold transplantation	RAW_FILE_NAME(Raw file name)=NEG_N755.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C711	Sample source:spinal cord tissue | Injection order:81 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C711.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C710	Sample source:spinal cord tissue | Injection order:82 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C710.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_C709	Sample source:spinal cord tissue | Injection order:83 | Treatment:scaffold-only transplantation	RAW_FILE_NAME(Raw file name)=NEG_C709.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M708	Sample source:spinal cord tissue | Injection order:84 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M708.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M758	Sample source:spinal cord tissue | Injection order:86 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M758.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	NEG_M762	Sample source:spinal cord tissue | Injection order:87 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=NEG_M762.wiff; ion mode=negtive mode
SUBJECT_SAMPLE_FACTORS           	-	POS_M728	Sample source:spinal cord tissue | Injection order:9 | Treatment:spinal cord injury model (SCI model)	RAW_FILE_NAME(Raw file name)=POS_M728.wiff; ion mode=positive mode
#COLLECTION
CO:COLLECTION_SUMMARY            	This study investigates the metabolic regulatory effects of neural stem cell
CO:COLLECTION_SUMMARY            	transplantation in spinal cord injury (SCI). The rat SCI model was established
CO:COLLECTION_SUMMARY            	as below: A laminectomy was performed at vertebral levels T7-T9 to expose the
CO:COLLECTION_SUMMARY            	spinal cord. Then a 3-mm long segment of spinal cord tissue was completely
CO:COLLECTION_SUMMARY            	transected. Sham-operated rats received a laminectomy only. For cell
CO:COLLECTION_SUMMARY            	transplantation, NSCs (1 × 10^6 cells in 20 μL of normal saline) were loaded
CO:COLLECTION_SUMMARY            	into a pre-sterilized multi-channel collagen scaffold (3 × 3 × 3 mm)
CO:COLLECTION_SUMMARY            	and engrafted to the cavity at the injury site. Three days after spinal cord
CO:COLLECTION_SUMMARY            	injury, the rats were sacrificed and dissected. Approximately 2 cm of tissue
CO:COLLECTION_SUMMARY            	surrounding the injury site was collected, rapidly frozen in liquid nitrogen,
CO:COLLECTION_SUMMARY            	and stored at -80°C. After the collection of all experimental tissues, the
CO:COLLECTION_SUMMARY            	collected spinal cord tissues were cut and weighed, with each sample
CO:COLLECTION_SUMMARY            	approximately 50 mg, and placed in 2 ml centrifuge tubes stored on ice awaiting
CO:COLLECTION_SUMMARY            	further pre-processing.
CO:SAMPLE_TYPE                   	Spinal cord
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	A laminectomy was performed at vertebral levels T7-T9 to expose the spinal cord.
TR:TREATMENT_SUMMARY             	Then a 3-mm long segment of spinal cord tissue was completely transected.
TR:TREATMENT_SUMMARY             	Sham-operated rats received a laminectomy only. For cell transplantation, neural
TR:TREATMENT_SUMMARY             	stem cells (1 × 10^6 cells in 20 μL of normal saline) were loaded into a
TR:TREATMENT_SUMMARY             	pre-sterilized multi-channel collagen scaffold (3 × 3 × 3 mm) and
TR:TREATMENT_SUMMARY             	engrafted to the cavity at the injury site.
TR:TREATMENT                     	cell transplantation
TR:TREATMENT_COMPOUND            	neural stem cells (NSCs)
TR:TREATMENT_ROUTE               	In situ transplantation
TR:TREATMENT_DOSE                	1 × 10^6 cells in 20 μL of normal saline per rat
TR:TREATMENT_DOSEVOLUME          	1 × 10^6 cells in 20 μL of normal saline per rat
TR:TREATMENT_DOSEDURATION        	1 × 10^6 cells in 20 μL of normal saline per rat
TR:TREATMENT_VEHICLE             	normal saline
TR:ANIMAL_ANESTHESIA             	Isoflurane
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Approximately 50 mg of each spinal cord tissue sample was weighed and
SP:SAMPLEPREP_SUMMARY            	homogenized in ice-cold 80% methanol (1:20, tissue weight (mg): solvent volume
SP:SAMPLEPREP_SUMMARY            	(μL)) using a tissue grinder. Homogenates were incubated at -40 °C for 4 hours
SP:SAMPLEPREP_SUMMARY            	and subsequently centrifugated at 13000 × g for 20 minutes at 4°C. The
SP:SAMPLEPREP_SUMMARY            	supernatant was collected, dried using a centrifugal concentrator, and stored at
SP:SAMPLEPREP_SUMMARY            	-80 °C. Prior to metabolomic analysis, all dried samples were redissolved and
SP:SAMPLEPREP_SUMMARY            	processed identically. A (QC) sample from all spinal cord samples was prepared
SP:SAMPLEPREP_SUMMARY            	for monitoring the stability of the analysis.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Chromatographic Separation: Liquid chromatography was performed using a Shimadzu
CH:CHROMATOGRAPHY_SUMMARY        	ExionLC system equipped with a Waters ACQUITY HSS T3 column (2.1 × 100 mm, 1.8
CH:CHROMATOGRAPHY_SUMMARY        	μm). The mobile phase consisted of (A) 0.1% formic acid in water and (B) 0.1%
CH:CHROMATOGRAPHY_SUMMARY        	formic acid in acetonitrile. The optimized ultra-high-performance liquid
CH:CHROMATOGRAPHY_SUMMARY        	chromatography (UHPLC) gradient elution program was as follows: 0–1.5 min,
CH:CHROMATOGRAPHY_SUMMARY        	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
CH:CHROMATOGRAPHY_SUMMARY        	min, 99.0% B. The flow rate was maintained at 0.30 ml/min, and the column
CH:CHROMATOGRAPHY_SUMMARY        	temperature was set at 40°C. A 2 μl aliquot of each sample was injected per
CH:CHROMATOGRAPHY_SUMMARY        	run. Samples were analyzed in a random order, with a pooled QC sample inserted
CH:CHROMATOGRAPHY_SUMMARY        	after every six test samples.
CH:INSTRUMENT_NAME               	Shimadzu ExionLC system
CH:COLUMN_NAME                   	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
CH:COLUMN_TEMPERATURE            	40°C
CH: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;
CH:FLOW_GRADIENT                 	16.5–16.6 min, 1.0% to 99% B, 16.6-20.0 min, 99.0% B.
CH:FLOW_RATE                     	0.30 mL/min
CH:SOLVENT_A                     	100% Water; 0.1% formic acid
CH:SOLVENT_B                     	100% Acetonitrile; 0.1% formic acid
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	ABI Sciex 5600+ TripleTOF
MS:INSTRUMENT_TYPE               	Triple TOF
MS:MS_TYPE                       	ESI
MS:MS_COMMENTS                   	The full scan covered a mass range from m/z 50 to 1000 Da. Ion spray voltages of
MS:MS_COMMENTS                   	+5500V for positive ion mode and -4500V for negative ion mode. Nitrogen was used
MS:MS_COMMENTS                   	as the nebulizer, heater and curtain gas at constant flow rates of 55, 55 and 35
MS:MS_COMMENTS                   	psi, respectively. MS/MS data was acquired using an information-dependent
MS:MS_COMMENTS                   	acquisition approach in high-sensitivity mode and real-time dynamic background
MS:MS_COMMENTS                   	subtraction. Collision was set at 35eV with a spread of 10eV. Mass calibration
MS:MS_COMMENTS                   	was automatically performed by the calibrant delivery system, which infused the
MS:MS_COMMENTS                   	atmospheric pressure chemical ionization (APCI) calibration solution every 5
MS:MS_COMMENTS                   	samples.
MS:ION_MODE                      	POSITIVE
MS:MS_RESULTS_FILE               	ST004170_AN006922_Results.txt	UNITS:peak area	Has m/z:Yes	Has RT:Yes	RT units:Minutes
#END