Summary of Study ST002989
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 PR001861. The data can be accessed directly via it's Project DOI: 10.21228/M85B0W 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 | ST002989 |
| Study Title | Targeting NPM1 Epigenetically Promotes Post-infarction Cardiac Repair by Reprogramming Reparative Macrophage Metabolism |
| Study Summary | Reparative macrophages play a crucial role in limiting excessive fibrosis and promoting cardiac repair after myocardial infarction (MI), highlighting the significance of enhancing their reparative phenotype for wound healing. Metabolic adaptation orchestrates the phenotypic transition of macrophages; however, the precise mechanisms governing metabolic reprogramming of cardiac reparative macrophages remain poorly understood. In this study, we investigated the role of Nucleophosmin 1 (NPM1) in the metabolic and phenotypic shift of cardiac macrophages in the context of MI, and explored the effect of targeting NPM1 for ischemic tissue repair. |
| Institute | Renji Hospital, Shanghai Jiao Tong University School of Medicine |
| Last Name | Zhan |
| First Name | Zhenzhen |
| Address | 160 Pujian Road, Shanghai, Shanghai, 200127, China |
| zhanzz2022@sjtu.edu.cn | |
| Phone | 86-21-61569249 |
| Submit Date | 2023-11-23 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-03-20 |
| Release Version | 1 |
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Project:
| Project ID: | PR001861 |
| Project DOI: | doi: 10.21228/M85B0W |
| Project Title: | Metabolic profiling of NPM1-deficient reparative BMDMs |
| Project Summary: | BMDMs (1×107) were either induced toward the reparative phenotype as described above or left unstimulated. These BMDMs were then used to perform a metabolomics assay at Shanghai Biotree Biotech Co. Ltd. (China). Briefly, for each sample, 500 μl precooled MeOH/H2O (3/1, v/v) was added in. The samples were then vortexed for 30 sec. After precooling in dry ice, the samples were frozen and thawed three times in liquid nitrogen. They were then vortexed for 30 sec and sonicated for 15 min in an ice-water bath. Next, as a subsequent step, the samples were incubated at -40 °C for 1 h and centrifuged at 12000 rpm for 15 min at 4 °C (RCF = 13800 g, R = 8.6 cm). Afterwards, an aliquot of 400 μl of clear supernatant was collected and dried by spinning. As a reconstitution solution, mix 200 ml of ultrapure water with the residue. The reconstituted samples were vortexed before passing through the filter of the centrifuge tube, after which they were transferred to inserts in injection vials for HPLC-MS/MS analysis. The HPIC separation was carried out using an Thermo Scientific Dionex ICS-6000 HPIC System (Thermo Scientific), equipped with Dionex IonPac AS11-HC (2× 250 mm) and AG11-HC (2 mm×50 mm) columns. An AB SCIEX 6500 QTRAP+ triple quadrupole mass spectrometer (AB Sciex), equipped with an electrospray ionization (ESI) interface, in multiple reaction monitoring (MRM) mode, was applied for assay development. AB SCIEX Analyst Work Station Software (1.6.3 AB SCIEX), MultiQuant 3.0.3. software and Chromeleon7 were employed for MRM data acquisition and processing. The finalized dataset, inclusive of compound name, sample name, and concentration, was imported into SIMCA 16.0.2 software (Sartorius Stedim Data Analytics AB, Umea, Sweden) for comprehensive multivariate analysis. The data were subjected to scaling and logarithmic transformation to mitigate the effects of noise and excessive variance of the variables. After that, we utilized the R packages tidyverse, dplyr, magrittr, ggplot2, and ggrepel for data analysis and the construction of a volcano plot. Additionally, the R packages circlize and reshape2 were employed in the creation of a chord diagram. For the generation of a heatmap, we made use of the R package pheatmap. |
| Institute: | Renji Hospital, Shanghai Jiao Tong University School of Medicine |
| Last Name: | Zhan |
| First Name: | Zhenzhen |
| Address: | 160 Pujian Road, Shanghai, Shanghai, 200127, China |
| Email: | zhanzz2022@sjtu.edu.cn |
| Phone: | 86-21-61569249 |
