Summary of Study ST001415

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 PR000971. The data can be accessed directly via it's Project DOI: 10.21228/M85X14 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.

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Study ID	ST001415
Study Title	Multi-omic profiling of primary mouse neutrophils reveals a pattern of sex and age-related functional regulation
Study Summary	Neutrophils are the most abundant white blood cells in humans and constitute one of the first lines of defense in the innate immune response. Neutrophils are extremely short-lived cells, which survive less than a day after reaching terminal differentiation. Thus, little is known about how organismal aging, rather than the daily cellular aging process, may impact neutrophil biology. In addition, accumulating evidence suggests that both immunity and organismal aging are extremely sex-dimorphic. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male animals, at the transcriptomic, metabolomic and lipidomic levels. Importantly, we identify widespread age-related and sex-dimorphic regulation of ‘omics’ in neutrophils, specifically regulation of chromatin metabolism. We leverage machine-learning and identify candidate molecular drivers of age-related and sex-dimorphic transcriptional regulation of neutrophils. We leverage our resource to predict increased levels/release of neutrophil elastase in male mice. To date, this dataset represents the largest multi-omic resource for the study of neutrophils across biological sex and ages. This resource identifies molecular states linked to neutrophil characteristics linked to organismal age or sex, which could be leveraged to improve immune responses across individuals.
Institute	Stanford University
Last Name	Contrepois
First Name	Kevin
Address	300 Pasteur Dr
Email	kcontrep@stanford.edu
Phone	6506664538
Submit Date	2020-06-30
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2021-06-30
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP001497
Sampleprep Summary:	Metabolites and lipids were extracted from neutrophil cell pellets and analyzed in a randomized order. Extraction was performed using a biphasic separation protocol with ice-cold methanol, methyl tert-butyl ether (MTBE) and water (Contrepois et al., 2018). Briefly, 300μL of methanol spiked-in with 54 deuterated internal standards provided with the Lipidyzer platform (SCIEX, cat #5040156, LPISTDKIT-101) was added to the cell pellet, samples were vigorously vortexed for 20 seconds and sonicated in a water bath 3 times for 30 seconds on ice. Lipids were solubilized by adding 1000μL of MTBE and incubated under agitation for 1h at 4°C. After addition of 250μL of ice-cold water, the samples were vortexed for 1 min and centrifuged at 14,000g for 5 min at 20°C. The upper phase containing the lipids was then collected and dried down under nitrogen. The dry lipid extracts were reconstituted with 300μL of 10 mM ammonium acetate in 9:1 methanol:toluene for analaysis. The lower phase containing metabolites was subjected to further protein precipitation by adding 4 times of ice-cold 1:1:1 isopropanol:acetonitrile:water spiked in with 17 labeled internal standards and incubating for 2 hours at -20°C. The supernatant was dried down to completion under nitrogen and re-suspended in 100μL of 1:1 MeOH:Water for analysis.

Sampleprep ID:

SP001497

Sampleprep Summary:

Metabolites and lipids were extracted from neutrophil cell pellets and analyzed in a randomized order. Extraction was performed using a biphasic separation protocol with ice-cold methanol, methyl tert-butyl ether (MTBE) and water (Contrepois et al., 2018). Briefly, 300μL of methanol spiked-in with 54 deuterated internal standards provided with the Lipidyzer platform (SCIEX, cat #5040156, LPISTDKIT-101) was added to the cell pellet, samples were vigorously vortexed for 20 seconds and sonicated in a water bath 3 times for 30 seconds on ice. Lipids were solubilized by adding 1000μL of MTBE and incubated under agitation for 1h at 4°C. After addition of 250μL of ice-cold water, the samples were vortexed for 1 min and centrifuged at 14,000g for 5 min at 20°C. The upper phase containing the lipids was then collected and dried down under nitrogen. The dry lipid extracts were reconstituted with 300μL of 10 mM ammonium acetate in 9:1 methanol:toluene for analaysis. The lower phase containing metabolites was subjected to further protein precipitation by adding 4 times of ice-cold 1:1:1 isopropanol:acetonitrile:water spiked in with 17 labeled internal standards and incubating for 2 hours at -20°C. The supernatant was dried down to completion under nitrogen and re-suspended in 100μL of 1:1 MeOH:Water for analysis.