Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Interferon-Gamma- and Murine-CMV-Activated Primary Macrophages

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Nigel Binns

PROVIDER: E-GEOD-42505 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The transcription factor STAT-1 couples macrophage synthesis of 25-hydroxycholesterol to the interferon antiviral response.

Blanc Mathieu M Hsieh Wei Yuan WY Robertson Kevin A KA Kropp Kai A KA Forster Thorsten T Shui Guanghou G Lacaze Paul P Watterson Steven S Griffiths Samantha J SJ Spann Nathanael J NJ Meljon Anna A Talbot Simon S Krishnan Kathiresan K Covey Douglas F DF Wenk Markus R MR Craigon Marie M Ruzsics Zsolts Z Haas Jürgen J Angulo Ana A Griffiths William J WJ Glass Christopher K CK Wang Yuqin Y Ghazal Peter P

Immunity 20121227 1

Recent studies suggest that the sterol metabolic network participates in the interferon (IFN) antiviral response. However, the molecular mechanisms linking IFN with the sterol network and the identity of sterol mediators remain unknown. Here we report a cellular antiviral role for macrophage production of 25-hydroxycholesterol (cholest-5-en-3β,25-diol, 25HC) as a component of the sterol metabolic network linked to the IFN response via Stat1. By utilizing quantitative metabolome profiling of all ...[more]

PMID: 23273843

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Project description:To enable successful SLC function deorphanization we aimed to select a minimal number of cell lines covering expression of as many SLCs as possible. Based on a publicly available RNA-Seq dataset of 675 cell lines (Klijn C. et al, Nat. Biotechnol. 2015) we selected a set of 6 adherent human cell lines (HCT 116, Huh 7, LS180, MDA MB 468, SK MEL 28, 1321N1) cumulatively covering expression (TPM>1) of about 80% of all human SLCs. These cell lines will be used to generate SLC-knockout and SLC-overexpressing single cell clones. Additionally, Jump-In T-REx HEK293 cells will be used for generating SLC-overexpression cell lines. In order to characterize the expressed proteome of these parental cell lines, we performed extensive proteomic profiling using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Mass spectra were acquired on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific) in data-dependent acquisition (DDA) mode. Instrument performance was monitored by a quality control routine using BSA- and HeLa digest standards. Data was analyzed using Thermo Proteome Discoverer 2.3 software. This data release consist of (1) RAW mass spectrometry data files generated by the instrument per fraction, (2) ProteomeDiscoverer result files containing all Peptide-Spectrum-Matches (PSMs), peptide and protein grouping, scoring and confidence values, as well as abundance values from label-free-quantitation (LFQ). As RESOLUTE will generate a significant number of protein-protein interaction data sets (AP-MS and BioID), the presented whole proteome profiling data set can serve as a reference core proteome data set, providing I) technical information on detected and expressed tryptic peptides and proteins; and II) provide valuable information on quantitative distribution of i.e. bait and prey proteins in the different cell lines. In conjunction with the other Omics data sets, like the previously published transcriptomics data, the characterization of the proteome will complement and enable valuable insight into the biological state of the investigated cell lines under default culturing conditions. Furthermore, members of the research community might apply advanced analyses with a focus out of the scope of the RESOLUTE project (e.g. PTM analysis).

Dataset Information

Interferon-Gamma- and Murine-CMV-Activated Primary Macrophages

Publications

The transcription factor STAT-1 couples macrophage synthesis of 25-hydroxycholesterol to the interferon antiviral response.

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