Summary of study ST001341

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 PR000914. The data can be accessed directly via it's Project DOI: 10.21228/M8JH69 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 IDST001341
Study TitleC56BL6 BMDM stimulated with different TLRs W/O acetylated LDL (part-II)
Study TypeAcetylated LDL
Study SummaryC57BL6 bone marrow derived macrophages were preloaded with 50 ug/mL of acetylated LDL and stimulated with TLR2, TLR3, TLR4, TLR7, and TLR9 ligands for 48 h.
Institute
University of California, Los Angeles
DepartmentMIMG
LaboratoryBensinger lab
Last NameBensinger
First NameSteven
AddressUniversity of California, Los Angeles
Emailbensingerlab@gmail.com
Phone3102061016
Submit Date2020-04-01
Raw Data AvailableYes
Raw Data File Type(s).mzXML
Analysis Type DetailLC-MS
Release Date2020-07-07
Release Version1
Steven Bensinger Steven Bensinger
https://dx.doi.org/10.21228/M8JH69
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000914
Project DOI:doi: 10.21228/M8JH69
Project Title:Toll-like receptors induce signal specific reprogramming of the macrophage lipidome
Institute:University of California, Los Angeles
Last Name:Bensinger
First Name:Steven
Email:bensingerlab@gmail.com

Subject:

Subject ID:SU001415
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL6/J
Age Or Age Range:8-12
Gender:Male

Factors:

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

mb_sample_id local_sample_id Treatment
SA097634NT_1NT
SA097635NT_4NT
SA097636NT_3NT
SA097637NT_2NT
SA097638NT+ACLDL_4NT+ACLDL
SA097639NT+ACLDL_1NT+ACLDL
SA097640NT+ACLDL_3NT+ACLDL
SA097641NT+ACLDL_2NT+ACLDL
SA097642TLR2_4TLR2
SA097643TLR2_2TLR2
SA097644TLR2_3TLR2
SA097645TLR2_1TLR2
SA097646TLR2+ACLDL_3TLR2+ACLDL
SA097647TLR2+ACLDL_4TLR2+ACLDL
SA097648TLR2+ACLDL_2TLR2+ACLDL
SA097649TLR2+ACLDL_1TLR2+ACLDL
SA097650TLR3_2TLR3
SA097651TLR3_4TLR3
SA097652TLR3_3TLR3
SA097653TLR3_1TLR3
SA097654TLR3+ACLDL_2TLR3+ACLDL
SA097655TLR3+ACLDL_3TLR3+ACLDL
SA097656TLR3+ACLDL_4TLR3+ACLDL
SA097657TLR3+ACLDL_1TLR3+ACLDL
SA097658TLR4_1TLR4
SA097659TLR4_2TLR4
SA097660TLR4_4TLR4
SA097661TLR4_3TLR4
SA097662TLR4+ACLDL_3TLR4+ACLDL
SA097663TLR4+ACLDL_4TLR4+ACLDL
SA097664TLR4+ACLDL_1TLR4+ACLDL
SA097665TLR4+ACLDL_2TLR4+ACLDL
SA097666TLR7_4TLR7
SA097667TLR7_3TLR7
SA097668TLR7_1TLR7
SA097669TLR7_2TLR7
SA097670TLR7+ACLDL_4TLR7+ACLDL
SA097671TLR7+ACLDL_3TLR7+ACLDL
SA097672TLR7+ACLDL_1TLR7+ACLDL
SA097673TLR7+ACLDL_2TLR7+ACLDL
SA097674TLR9_4TLR9
SA097675TLR9_2TLR9
SA097676TLR9_3TLR9
SA097677TLR9_1TLR9
SA097678TLR9+ACLDL_4TLR9+ACLDL
SA097679TLR9+ACLDL_2TLR9+ACLDL
SA097680TLR9+ACLDL_1TLR9+ACLDL
SA097681TLR9+ACLDL_3TLR9+ACLDL
Showing results 1 to 48 of 48

Collection:

Collection ID:CO001410
Collection Summary:Day 6 BMDMs were seeded at a density of 9x105 cell/well in 6 well dishes (Fisher 08-772-1B). On day 8, BMDM were mock-treated (media change) or co-treated with ligands as described below in 5% BMDM media for 48 h. Prior to collection, cell number was assessed by imaging as described below. After removal of culturing media, 1 mL of ice-cold PBS was added into each well and cells were scraped with cell lifters and spun down in glass tubes at 365g for 5 min at 4°C.
Sample Type:Macrophages

Treatment:

Treatment ID:TR001430
Treatment Summary:BMDMs were seeded at a density of 9x105 cell/well in 6 well dishes (Fisher 08-772-1B). On day 8, BMDM were first pre-loaded with 50 ug/mL of acetylated-LDL for 2 h, followed by TLR2, TLR3, TLR4, TLR7, or TLR9 ligands stimulation in 5% FBS BMDM media for 48 h.

Sample Preparation:

Sampleprep ID:SP001423
Sampleprep Summary:A modified Bligh and Dyer extraction (Bligh and Dyer, 1959) was carried out on samples. Prior to biphasic extraction, a 13-lipid class Lipidyzer Internal Standard Mix is added to each sample (AB Sciex, 5040156). Following two successive extractions, pooled organic layers were dried down in a Genevac EZ-2 Elite. Lipid samples were resuspended in 1:1 methanol/dichloromethane with 10 mM Ammonium Acetate and transferred to robovials (Thermo 10800107) for analysis.

Combined analysis:

Analysis ID AN002235
Analysis type MS
Chromatography type None (Direct infusion)
Chromatography system none
Column none
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTRAP with SelexION
Ion Mode UNSPECIFIED
Units nmol per 10e7 cells

Chromatography:

Chromatography ID:CH001641
Instrument Name:none
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002081
Analysis ID:AN002235
Instrument Name:ABI Sciex 5500 QTRAP with SelexION
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Lipidyzer Workflow Manager 1.0 Samples are normalized to cell count
Ion Mode:UNSPECIFIED
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