Summary of project PR001861
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
| 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 |
Summary of all studies in project PR001861
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST002989 | Targeting NPM1 Epigenetically Promotes Post-infarction Cardiac Repair by Reprogramming Reparative Macrophage Metabolism | Mus musculus | Renji Hospital, Shanghai Jiao Tong University School of Medicine | MS | 2024-03-20 | 1 | 16 | Uploaded data (3.1M)* |
