Summary of Study ST004537

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 PR002861. The data can be accessed directly via it's Project DOI: 10.21228/M8VC3K This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST004537
Study TitleC8 positive-mode LC–MS lipidomics of BMDM and PMN: WT vs KO (n=22)
Study SummaryWe performed LC–MS lipidomics to quantify lipid remodeling associated with Tet2 KO in myeloid cells. Lipids were extracted from bone marrow–derived macrophages (BMDM; 7 WT and 7 KO replicates) and neutrophils/PMN (4 WT and 4 KO replicates) from murine bone marrow (BMDMD) or zymosan-induced peritoneum (PM) and analyzed using C8 reversed-phase liquid chromatography coupled to positive-ion electrospray mass spectrometry. This dataset includes raw LC–MS files (mzML and vendor raw) and processed lipid abundance tables used for the analyses reported in the associated manuscript “Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis ”.
Institute
Harvard Medical School
Last NameKim
First NamePeter Geon
Address360 Longwood Ave, LC8202 Boston, MA 02215 USA
Emailgkim0@partners.org
Phone6175254942
Submit Date2026-01-08
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2026-01-16
Release Version1
Peter Geon Kim Peter Geon Kim
https://dx.doi.org/10.21228/M8VC3K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002861
Project DOI:doi: 10.21228/M8VC3K
Project Title:Lipidomics dataset for "Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis"
Project Summary:This project deposits LC–MS lipidomics raw and processed data supporting the manuscript "Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis". Lipid profiles were measured using C8 reversed-phase chromatography and positive-ion MS in mouse macrophages annd neutrophils, comparing WT versus Tet2 KO.
Institute:Harvard Medical School
Department:Department of Medical Oncology at Dana Farber Cancer Institute
Laboratory:Ebert
Last Name:Peter Geon
First Name:Kim
Address:360 Longwood Ave, LC8202 Boston, MA 02215 USA
Email:gkim0@partners.org
Phone:6175254942

Subject:

Subject ID:SU004716
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 Sample source cell_type genotype
SA537937BMDM_KO6BMDM BMDM KO
SA537938BMDM_KO2BMDM BMDM KO
SA537939BMDM_KO7BMDM BMDM KO
SA537940BMDM_KO1BMDM BMDM KO
SA537941BMDM_KO5BMDM BMDM KO
SA537942BMDM_KO3BMDM BMDM KO
SA537943BMDM_KO4BMDM BMDM KO
SA537944BMDM_WT7BMDM BMDM WT
SA537945BMDM_WT6BMDM BMDM WT
SA537946BMDM_WT5BMDM BMDM WT
SA537947BMDM_WT4BMDM BMDM WT
SA537948BMDM_WT3BMDM BMDM WT
SA537949BMDM_WT2BMDM BMDM WT
SA537950BMDM_WT1BMDM BMDM WT
SA537951PMN_KO2PMN PMN KO
SA537952PMN_KO3PMN PMN KO
SA537953PMN_KO4PMN PMN KO
SA537954PMN_KO1PMN PMN KO
SA537955PMN_WT1PMN PMN WT
SA537956PMN_WT2PMN PMN WT
SA537957PMN_WT3PMN PMN WT
SA537958PMN_WT4PMN PMN WT
Showing results 1 to 22 of 22

Collection:

Collection ID:CO004709
Collection Summary:For lipidomics or metabolomics experiments, mouse neutrophils were obtained from transplanted WT or Tet2 KO mice 4 weeks after transplantation, isolated 12 hours after zymosan 1mg i.p. injection using the neutrophil isolation kit (Miltenyi, 130-097-658). BMDMs were obtained from the bone marrow using differentiation method using MCSF 20ng/ml in DMEM / 10% FCS / PSG fforr 7-10 days
Sample Type:Bone marrow

Treatment:

Treatment ID:TR004725
Treatment Summary:Samples were generated from WT and conditional Tet2 knockout (KO) mice (Cre-lox model). Genotypes were determined by PCR-based genotyping, and Cre-mediated recombination status was confirmed per standard lab procedures. BMDMs and PMNs were prepared as described in the associated manuscript and BMDMs were collected under basal conditions from the bone marrow. PMNs were collected 12 hours after 1mg intraperitoneal zymosan injection using the Neutrophil Isolation Kit, mouse (Miltenyi).

Sample Preparation:

Sampleprep ID:SP004722
Sampleprep Summary:Cell pellets were extracted for lipidomics using isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids) as an internal standard. Extracts were centrifuged and supernatants were injected for LC–MS analysis (C8 reversed-phase, positive-ion mode).

Combined analysis:

Analysis ID AN007621
Chromatography ID CH005780
MS ID MS007318
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu Nexera X2
Column Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap
Ion Mode POSITIVE
Units peak area (a.u.)

Chromatography:

Chromatography ID:CH005780
Instrument Name:Shimadzu Nexera X2
Column Name:Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
Column Temperature:40
Flow Gradient:0–1 min: 80% A (20% B) isocratic; 1–3 min: linear to 80% B (20% A); 3–10 min: linear to 100% B; 10–13 min: hold 100% B
Flow Rate:450uL/min
Solvent A:95:5:0.1 vol/vol/vol 10mM ammonium acetate/methanol/formic acid
Solvent B:99.9:0.1 vol/vol methanol/formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS007318
Analysis ID:AN007621
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS acquisition comments: Electrospray ionization (ESI) in positive mode; full-scan MS over m/z 200–1100 at 70,000 resolution with 3 Hz data acquisition. Sheath gas 50; sweep gas 5; in-source CID 5 eV; spray voltage 3 kV; capillary temperature 300°C; heater temperature 300°C; S-lens RF 60; microscans 1; AGC target 1e6; maximum ion time 100 ms. Data processing comments: Raw data were processed using Thermo TraceFinder for targeted peak integration with manual review of a subset of identified lipids, and Progenesis QI (Nonlinear Dynamics) for peak detection and integration of known and unknown lipids/features. Software/procedures used for feature assignments: Lipid identities were assigned by comparison to reference plasma extracts; lipids are denoted by total acyl-chain carbons and total double bonds
Ion Mode:POSITIVE
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