Summary of Study ST001345

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 IDST001345
Study TitleC56BL6 WT or IFNARKO BMDM stimulated with different TLRs (part-V)
Study SummaryWT control or IFNAR deficient bone marrow derived macrophages were stimulated with IFNb, TLR3, IFNg, TLR4, and TLR4+IFNg 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)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:SU001419
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 Genotype
SA097808IFNB_IFNARKO_3IFNB IFNAR-/-
SA097809IFNB_IFNARKO_1IFNB IFNAR-/-
SA097810IFNB_IFNARKO_2IFNB IFNAR-/-
SA097811IFNB_IFNARKO_4IFNB IFNAR-/-
SA097812IFNB_WT_3IFNB WT
SA097813IFNB_WT_4IFNB WT
SA097814IFNB_WT_2IFNB WT
SA097815IFNB_WT_1IFNB WT
SA097816IFNG_IFNARKO_4IFNG IFNAR-/-
SA097817IFNG_IFNARKO_2IFNG IFNAR-/-
SA097818IFNG_IFNARKO_3IFNG IFNAR-/-
SA097819IFNG_IFNARKO_1IFNG IFNAR-/-
SA097820IFNG_WT_3IFNG WT
SA097821IFNG_WT_4IFNG WT
SA097822IFNG_WT_2IFNG WT
SA097823IFNG_WT_1IFNG WT
SA097824NT_IFNARKO_3NT IFNAR-/-
SA097825NT_IFNARKO_4NT IFNAR-/-
SA097826NT_IFNARKO_2NT IFNAR-/-
SA097827NT_IFNARKO_1NT IFNAR-/-
SA097828NT_WT_2NT WT
SA097829NT_WT_3NT WT
SA097830NT_WT_1NT WT
SA097831NT_WT_4NT WT
SA097832TLR3_IFNARKO_2TLR3 IFNAR-/-
SA097833TLR3_IFNARKO_3TLR3 IFNAR-/-
SA097834TLR3_IFNARKO_1TLR3 IFNAR-/-
SA097835TLR3_IFNARKO_4TLR3 IFNAR-/-
SA097836TLR3_WT_3TLR3 WT
SA097837TLR3_WT_1TLR3 WT
SA097838TLR3_WT_2TLR3 WT
SA097839TLR3_WT_4TLR3 WT
SA097848TLR4_IFNARKO_2TLR4 IFNAR-/-
SA097849TLR4_IFNARKO_3TLR4 IFNAR-/-
SA097850TLR4_IFNARKO_4TLR4 IFNAR-/-
SA097851TLR4_IFNARKO_1TLR4 IFNAR-/-
SA097852TLR4_WT_1TLR4 WT
SA097853TLR4_WT_2TLR4 WT
SA097854TLR4_WT_3TLR4 WT
SA097855TLR4_WT_4TLR4 WT
SA097840TLR4IFNG_IFNARKO_3TLR4IFNG IFNAR-/-
SA097841TLR4IFNG_IFNARKO_1TLR4IFNG IFNAR-/-
SA097842TLR4IFNG_IFNARKO_4TLR4IFNG IFNAR-/-
SA097843TLR4IFNG_IFNARKO_2TLR4IFNG IFNAR-/-
SA097844TLR4IFNG_WT_3TLR4IFNG WT
SA097845TLR4IFNG_WT_4TLR4IFNG WT
SA097846TLR4IFNG_WT_2TLR4IFNG WT
SA097847TLR4IFNG_WT_1TLR4IFNG WT
Showing results 1 to 48 of 48

Collection:

Collection ID:CO001414
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:TR001434
Treatment Summary:WT or IFNAR 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 IFNB, TLR3, IFNG, TLR4, and TLR4+IFNg ligands in 5% FBS BMDM media for 48 h.

Sample Preparation:

Sampleprep ID:SP001427
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 AN002239
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:CH001645
Instrument Name:none
Column Name:none
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS002085
Analysis ID:AN002239
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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