Summary of Study ST001343

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 IDST001343
Study TitleC56BL6 WT or TRIFKO BMDM stimulated with different TLRs (part-III)
Study TypeWT vs TRIF deficient macrophages
Study SummaryWT control or TRIF deficient bone marrow derived macrophages were stimulated with TLR2, TLR3, and TLR4 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)mzML
Analysis Type DetailMS(Dir. Inf.)
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:SU001417
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 Genotype
SA097730NT_TRIFKO_3NT TRIF-/-
SA097731NT_TRIFKO_4NT TRIF-/-
SA097732NT_TRIFKO_1NT TRIF-/-
SA097733NT_TRIFKO_2NT TRIF-/-
SA097734NT_WT_1NT WT
SA097735NT_WT_3NT WT
SA097736NT_WT_2NT WT
SA097737NT_WT_4NT WT
SA097738TLR2_TRIFKO_2TLR2 TRIF-/-
SA097739TLR2_TRIFKO_3TLR2 TRIF-/-
SA097740TLR2_TRIFKO_1TLR2 TRIF-/-
SA097741TLR2_TRIFKO_4TLR2 TRIF-/-
SA097742TLR2_WT_4TLR2 WT
SA097743TLR2_WT_1TLR2 WT
SA097744TLR2_WT_2TLR2 WT
SA097745TLR2_WT_3TLR2 WT
SA097746TLR3_TRIFKO_4TLR3 TRIF-/-
SA097747TLR3_TRIFKO_2TLR3 TRIF-/-
SA097748TLR3_TRIFKO_3TLR3 TRIF-/-
SA097749TLR3_TRIFKO_1TLR3 TRIF-/-
SA097750TLR3_ WT_2TLR3 WT
SA097751TLR3_ WT_1TLR3 WT
SA097752TLR3_ WT_4TLR3 WT
SA097753TLR4_TRIFKO_3TLR4 TRIF-/-
SA097754TLR4_TRIFKO_4TLR4 TRIF-/-
SA097755TLR4_TRIFKO_2TLR4 TRIF-/-
SA097756TLR4_WT_3TLR4 WT
SA097757TLR4_WT_1TLR4 WT
SA097758TLR4_WT_2TLR4 WT
SA097759TLR4_WT_4TLR4 WT
Showing results 1 to 30 of 30

Collection:

Collection ID:CO001412
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
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001432
Treatment Summary:WT or TRIF deficient BMDMs were seeded at a density of 9x105 cell/well in 6 well dishes (Fisher 08-772-1B). On day 8, BMDM were stimulated with TLR2, TLR3, or TLR4 ligands in 5% FBS BMDM media for 48 h.

Sample Preparation:

Sampleprep ID:SP001425
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 AN002237
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:CH001643
Instrument Name:none
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002083
Analysis ID:AN002237
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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