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.

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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.

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Study IDST002989
Study TitleTargeting NPM1 Epigenetically Promotes Post-infarction Cardiac Repair by Reprogramming Reparative Macrophage Metabolism
Study SummaryReparative 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 NameZhan
First NameZhenzhen
Address160 Pujian Road, Shanghai, Shanghai, 200127, China
Emailzhanzz2022@sjtu.edu.cn
Phone86-21-61569249
Submit Date2023-11-23
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-03-20
Release Version1
Zhenzhen Zhan Zhenzhen Zhan
https://dx.doi.org/10.21228/M85B0W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

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

Subject:

Subject ID:SU003102
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA325750G2.4Npm1-knockout
SA325751G2.3Npm1-knockout
SA325752G2.5Npm1-knockout
SA325753G2.7Npm1-knockout
SA325754G2.8Npm1-knockout
SA325755G2.2Npm1-knockout
SA325756G2.6Npm1-knockout
SA325757G2.1Npm1-knockout
SA325758G1.4Wild-type
SA325759G1.3Wild-type
SA325760G1.2Wild-type
SA325761G1.5Wild-type
SA325762G1.6Wild-type
SA325763G1.8Wild-type
SA325764G1.7Wild-type
SA325765G1.1Wild-type
Showing results 1 to 16 of 16

Collection:

Collection ID:CO003095
Collection Summary:BMDMs (1×10^7) were induced toward the reparative phenotype using recombinant murine IL-4.BMDMs were counted and washed with PBS.
Sample Type:Bone marrow

Treatment:

Treatment ID:TR003111
Treatment Summary:mouse bone marrow cells were flushed out from mouse femurs using RPMI 1640 and cultured in a complete RPMI 1640 medium (added with 10% fetal bovine serum and 1% penicillin/streptomycin) supplemented with 20 ng/ml M-CSF for 7 days to generate mature BMDMs. BMDMs were stimulated with 20 ng/ml IL-4 for 12 h to induce a reparative phenotype.

Sample Preparation:

Sampleprep ID:SP003108
Sampleprep Summary: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.

Combined analysis:

Analysis ID AN004909
Analysis type MS
Chromatography type Ion exchange
Chromatography system Thermo Scientific Dionex ICS-6000 HPIC
Column Dionex IonPac AS11-HC (250 × 2mm, 9um, 2000Ã) and AG11-HC (50 × 2 mm, 13um)
MS Type ESI
MS instrument type QTRAP
MS instrument name ABI Sciex 6500+
Ion Mode UNSPECIFIED
Units pmol

Chromatography:

Chromatography ID:CH003704
Instrument Name:Thermo Scientific Dionex ICS-6000 HPIC
Column Name:Dionex IonPac AS11-HC (250 × 2mm, 9um, 2000Ã) and AG11-HC (50 × 2 mm, 13um)
Column Temperature:30 ℃
Flow Gradient:0.15 mL/min: 0min:20%/80%, 3.01min:20%/80%,12min:50%/50%, 21min:100%/100%, 26min:100%/100%, 26.1min:20%/80%,0min:80%/20%, 30min:80%/20%
Flow Rate:0.15 mL/min
Solvent A:100 mM NaOH/water; water
Solvent B:water
Chromatography Type:Ion exchange
Solvent C:2 mM acetic acid in methanol

MS:

MS ID:MS004652
Analysis ID:AN004909
Instrument Name:ABI Sciex 6500+
Instrument Type:QTRAP
MS Type:ESI
MS Comments: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.
Ion Mode:UNSPECIFIED
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