Summary of study ST001344

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 IDST001344
Study TitleC56BL6 WT or MyD88KO BMDM stimulated with different TLRs (part-IV)
Study TypeWT vs MyD88 deficient macrophages
Study SummaryWT control or MyD88 deficient bone marrow derived macrophages were stimulated with TLR2, TLR3, TLR4, TLR7, and TLR9 ligands for 48 h.
Institute
University of California, Los Angeles
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:SU001418
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
SA097760NT_MYD88KO_3NT MyD88-/-
SA097761NT_MYD88KO_4NT MyD88-/-
SA097762NT_MYD88KO_1NT MyD88-/-
SA097763NT_MYD88KO_2NT MyD88-/-
SA097764NT_WT_1NT WT
SA097765NT_WT_3NT WT
SA097766NT_WT_2NT WT
SA097767NT_WT_4NT WT
SA097768TLR2_MYD88KO_2TLR2 MyD88-/-
SA097769TLR2_MYD88KO_4TLR2 MyD88-/-
SA097770TLR2_MYD88KO_1TLR2 MyD88-/-
SA097771TLR2_MYD88KO_3TLR2 MyD88-/-
SA097772TLR2_WT_4TLR2 WT
SA097773TLR2_WT_3TLR2 WT
SA097774TLR2_WT_2TLR2 WT
SA097775TLR2_WT_1TLR2 WT
SA097776TLR3_MYD88KO_2TLR3 MyD88-/-
SA097777TLR3_MYD88KO_4TLR3 MyD88-/-
SA097778TLR3_MYD88KO_3TLR3 MyD88-/-
SA097779TLR3_MYD88KO_1TLR3 MyD88-/-
SA097780TLR3_WT_4TLR3 WT
SA097781TLR3_WT_2TLR3 WT
SA097782TLR3_WT_1TLR3 WT
SA097783TLR3_WT_3TLR3 WT
SA097784TLR4_MYD88KO_1TLR4 MyD88-/-
SA097785TLR4_MYD88KO_3TLR4 MyD88-/-
SA097786TLR4_MYD88KO_4TLR4 MyD88-/-
SA097787TLR4_MYD88KO_2TLR4 MyD88-/-
SA097788TLR4_WT_1TLR4 WT
SA097789TLR4_WT_4TLR4 WT
SA097790TLR4_WT_2TLR4 WT
SA097791TLR4_WT_3TLR4 WT
SA097792TLR7_MYD88KO_2TLR7 MyD88-/-
SA097793TLR7_MYD88KO_3TLR7 MyD88-/-
SA097794TLR7_MYD88KO_1TLR7 MyD88-/-
SA097795TLR7_MYD88KO_4TLR7 MyD88-/-
SA097796TLR7_WT_4TLR7 WT
SA097797TLR7_WT_2TLR7 WT
SA097798TLR7_WT_1TLR7 WT
SA097799TLR7_WT_3TLR7 WT
SA097800TLR9_MYD88KO_1TLR9 MyD88-/-
SA097801TLR9_MYD88KO_3TLR9 MyD88-/-
SA097802TLR9_MYD88KO_2TLR9 MyD88-/-
SA097803TLR9_MYD88KO_4TLR9 MyD88-/-
SA097804TLR9_WT_3TLR9 WT
SA097805TLR9_WT_1TLR9 WT
SA097806TLR9_WT_2TLR9 WT
SA097807TLR9_WT_4TLR9 WT
Showing results 1 to 48 of 48

Collection:

Collection ID:CO001413
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:TR001433
Treatment Summary:WT or MyD88 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, TLR4, TLR7, or TLR9 ligands in 5% FBS BMDM media for 48 h.

Sample Preparation:

Sampleprep ID:SP001426
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 AN002238
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:CH001644
Instrument Name:none
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002084
Analysis ID:AN002238
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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