Summary of study ST001342

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 IDST001342
Study TitleTimecourse of C56BL6 BMDM stimulated with different TLRs (part-I)
Study TypeTimecourse
Study SummaryC57BL6 bone marrow derived macrophages were stimulated with TLR2, TLR3, TLR4, TLR7, and TLR9 ligands for 24 or 48 h.
Institute
University of California, Los Angeles
DepartmentMIMG
LaboratoryBensinger lab
Last NameBensinger
First NameSteven
AddressUniversity of California, Los Angeles
Emailbensingerlab@gmail.com
Phone310-206-1016
Submit Date2020-03-27
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:SU001416
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL6/J
Age Or Age Range:8-12
Gender:Male
Cell Passage Number:Primary

Factors:

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

mb_sample_id local_sample_id Treatment Time
SA097682NT_1NT 24
SA097683NT_4NT 24
SA097684NT_3NT 24
SA097685NT_2NT 24
SA097686NT_26NT 48
SA097687NT_28NT 48
SA097688NT_27NT 48
SA097689NT_25NT 48
SA097690TLR2_8TLR2 24
SA097691TLR2_7TLR2 24
SA097692TLR2_5TLR2 24
SA097693TLR2_6TLR2 24
SA097694TLR2_31TLR2 48
SA097695TLR2_32TLR2 48
SA097696TLR2_30TLR2 48
SA097697TLR2_29TLR2 48
SA097698TLR3_9TLR3 24
SA097699TLR3_10TLR3 24
SA097700TLR3_11TLR3 24
SA097701TLR3_12TLR3 24
SA097702TLR3_35TLR3 48
SA097703TLR3_36TLR3 48
SA097704TLR3_34TLR3 48
SA097705TLR3_33TLR3 48
SA097706TLR4_14TLR4 24
SA097707TLR4_13TLR4 24
SA097708TLR4_15TLR4 24
SA097709TLR4_16TLR4 24
SA097710TLR4_39TLR4 48
SA097711TLR4_40TLR4 48
SA097712TLR4_38TLR4 48
SA097713TLR4_37TLR4 48
SA097714TLR7_18TLR7 24
SA097715TLR7_20TLR7 24
SA097716TLR7_17TLR7 24
SA097717TLR7_19TLR7 24
SA097718TLR7_43TLR7 48
SA097719TLR7_44TLR7 48
SA097720TLR7_42TLR7 48
SA097721TLR7_41TLR7 48
SA097722TLR9_21TLR9 24
SA097723TLR9_22TLR9 24
SA097724TLR9_23TLR9 24
SA097725TLR9_24TLR9 24
SA097726TLR9_48TLR9 48
SA097727TLR9_45TLR9 48
SA097728TLR9_46TLR9 48
SA097729TLR9_47TLR9 48
Showing results 1 to 48 of 48

Collection:

Collection ID:CO001411
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:TR001431
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 mock-treated (media change) or co-treated with TLR2, TLR3, TLR4, TLR7, or TLR9 ligands in 5% FBS BMDM media for 24 or 48 h.

Sample Preparation:

Sampleprep ID:SP001424
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 AN002236
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:CH001642
Instrument Name:none
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002082
Analysis ID:AN002236
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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