Summary of Study ST002961
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 PR001842. The data can be accessed directly via it's Project DOI: 10.21228/M8MH8P 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 | ST002961 |
| Study Title | Analysis of Metabolites Secreted from Fibroblast Young Cells |
| Study Summary | In this experimental study, we aimed to uncover the factors in young cell secretions that trigger the reverse aging of mid-old cells, co-culturing them and observing a striking transformation, although we could not identify the specific factors responsible for this rejuvenation |
| Institute | Ajou University Medical Center |
| Last Name | Kim |
| First Name | Young Hwa |
| Address | 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea |
| skyblue32@nate.com | |
| Phone | +82-10-5153-3636 |
| Submit Date | 2023-11-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001842 |
| Project DOI: | doi: 10.21228/M8MH8P |
| Project Title: | Mid-Old Cells are Potential Target for Anti-aging Interventions in the Elderly |
| Project Summary: | The biological process of aging is thought to result in part from accumulation of senescent cells in organs. However, the present study identified a subset of fibroblasts and smooth muscle cells which are the major constituents of organ stroma neither proliferative nor senescent in tissues of the elderly, which we termed “mid-old status” cells. Upregulation of pro-inflammatory genes (IL1B and SAA1) and downregulation of anti-inflammatory genes (SLIT2 and CXCL12) were detected in mid-old cells. In the stroma, SAA1 promotes development of the inflammatory microenvironment via upregulation of MMP9, which decreases the stability of epithelial cells present on the basement membrane, decreasing epithelial cell function. Remarkably, the microenvironmental change and the functional decline of mid-old cells could be reversed by a young cell-originated protein, SLIT2. Our data identify functional reversion of mid-old cells as a potential method to prevent or ameliorate aspects of aging-related tissue dysfunction. |
| Institute: | Ajou University Medical Center |
| Last Name: | Kim |
| First Name: | Young Hwa |
| Address: | 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea |
| Email: | skyblue32@nate.com |
| Phone: | +82-10-5153-3636 |
Subject:
| Subject ID: | SU003074 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample_type |
|---|---|---|
| SA322379 | 20210624_AJU_M3 | Control sample |
| SA322380 | 20210624_AJU_M2 | Control sample |
| SA322381 | 20210624_AJU_M1 | Control sample |
| SA322382 | blank_20210624 | None |
| SA322383 | 20210624_AJU_Y2 | Test sample |
| SA322384 | 20210624_AJU_Y3 | Test sample |
| SA322385 | 20210624_AJU_Y1 | Test sample |
| Showing results 1 to 7 of 7 |
Collection:
| Collection ID: | CO003067 |
| Collection Summary: | The experiment was initiated by seeding the cells in a 100mm cell culture dish, followed by a 2-day incubation period, during which the culture medium was carefully extracted from the cell culture dish. Use a sterile technique to minimize contamination. Transfer the harvested culture medium to a suitable container. |
| Collection Protocol Filename: | Sample_collection_metabolite.pdf |
| Sample Type: | Cultured fibroblasts |
Treatment:
| Treatment ID: | TR003083 |
| Treatment Summary: | no treatment |
Sample Preparation:
| Sampleprep ID: | SP003080 |
| Sampleprep Summary: | Metabolites were extracted using 80% methanol. In brief, the samples were added with 80% methanol. After vortexing for 1 min and centrifugation at 2000×g for 10 min, supernatant was transferred to a new 1.5 mL tube and completely dried using a HyperVAC-MAX VC2200 centrifugal vacuum concentrator (Hanil Scientific Inc., Korea). Dried metabolite contents were reconstituted in 100 µL of 0.1% formic acid in water and then subjected to LC-MS/MS analysis. |
| Sampleprep Protocol Filename: | Sampleprep_metabolite.pdf |
Combined analysis:
| Analysis ID | AN004862 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity UHPLC |
| Column | Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm, 1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Q Exactive™ Hybrid Quadrupole-Orbitrap MS coupled with a 1290 Infinity UHPLC |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH003670 |
| Chromatography Summary: | See protocol file, LC_MS_method_metabolite.pdf |
| Methods Filename: | LC_MS_method_metabolite.pdf |
| Instrument Name: | Agilent 1290 Infinity UHPLC |
| Column Name: | Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm, 1.8um) |
| Column Temperature: | 320℃ |
| Flow Gradient: | 2.5% solvent B in 5 min, 2.5–12.5% solvent B in 29 min, 12.5–25% solvent B in 11 min, 25–37.5% solvent B in 11 min, 37.5-80% solvent B in 0.1 min, holding at 80% of solvent B in 13.9 min, 80–2.5% solvent B in 0.1 min, 2.5% solvent B for 19.9 min |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 0.1% formic acid in water |
| Solvent B: | 0.1% formic acid in 80% acetonitrile |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004606 |
| Analysis ID: | AN004862 |
| Instrument Name: | Q Exactive™ Hybrid Quadrupole-Orbitrap MS coupled with a 1290 Infinity UHPLC |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Obtained UHPLC-Orbitrap-MS/MS RAW files were processed using Compound Discoverer 3.1.1.12TM (Thermo Fisher Scientific, Waltham, MA, USA). Untargeted metabolomics workflow was used to perform retention time alignment and compound identification. Identification of compounds using mzCloud and ChemSpider |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_analysis_metabolite.pdf |
