Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA325757

Local Sample ID:	G2.1
Subject ID:	SU003102
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Select appropriate tab below to view additional metadata details:

Subject:

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

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
G2.1	SA325757	FL038739	Npm1-knockout	Genotype

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.

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