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
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 | 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. |
| 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 |
Select appropriate tab below to view additional metadata details:
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 |
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. |
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 |
Analysis:
| Analysis ID: | AN006922 |
| Analysis Type: | MS |
| Chromatography ID: | CH005257 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST004170_AN006922_Results.txt |
| Units: | peak area |
| Analysis ID: | AN006923 |
| Analysis Type: | MS |
| Chromatography ID: | CH005257 |
| Has Mz: | 1 |
| Has Rt: | 1 |
| Rt Units: | Minutes |
| Results File: | ST004170_AN006923_Results.txt |
| Units: | peak area |
