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      Data from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with Withaferin A (WA)

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          Abstract

          Mass spectrometry data collected in a study analyzing the effect of withaferin A (WA) on a mouse microglial (N9) cell line is presented in this article. Data was collected from SILAC-based quantitative analysis of lysates from mouse microglial cells treated with either WA or DMSO vehicle control. This article reports all the proteins that were identified in this analysis. The data presented here is related to the published research article on the effect of WA on the differential regulation of proteins in mouse microglial cells [1]. Mass spectrometry data has also been deposited in the ProteomeXchange with the identifier PXD003032.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

          Yoav Benjamini, Yosef Hochberg (1995)
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            Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.

            Shao-En Ong, Blagoy Blagoev, Irina Kratchmarova … (2002)
            Quantitative proteomics has traditionally been performed by two-dimensional gel electrophoresis, but recently, mass spectrometric methods based on stable isotope quantitation have shown great promise for the simultaneous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC, for stable isotope labeling by amino acids in cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins. Mammalian cell lines are grown in media lacking a standard essential amino acid but supplemented with a non-radioactive, isotopically labeled form of that amino acid, in this case deuterated leucine (Leu-d3). We find that growth of cells maintained in these media is no different from growth in normal media as evidenced by cell morphology, doubling time, and ability to differentiate. Complete incorporation of Leu-d3 occurred after five doublings in the cell lines and proteins studied. Protein populations from experimental and control samples are mixed directly after harvesting, and mass spectrometric identification is straightforward as every leucine-containing peptide incorporates either all normal leucine or all Leu-d3. We have applied this technique to the relative quantitation of changes in protein expression during the process of muscle cell differentiation. Proteins that were found to be up-regulated during this process include glyceraldehyde-3-phosphate dehydrogenase, fibronectin, and pyruvate kinase M2. SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system.
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              Identification and quantitative analysis of cellular proteins affected by treatment with withaferin a using a SILAC-based proteomics approach

              Malathi Narayan, Kent Seeley, Umesh K. Jinwal (2015)
              Withaferin A (WA) is a major bioactive compound isolated from the medicinal plant Withania somnifera Dunal, also known as "Ashwagandha". A number of published reports suggest various uses for WA including its function as an anti-inflammatory and anti-angiogenic drug molecule. The effects of WA at the molecular level in a cellular environment are not well understood. Knowledge of the molecular mechanism of action of WA could enhance its therapeutic value and may reveal novel pathways it may modulate.
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                Author and article information

                Contributors
                Umesh K. Jinwal
                Journal
                Journal ID (nlm-ta): Data Brief
                Journal ID (iso-abbrev): Data Brief
                Title: Data in Brief
                Publisher: Elsevier
                ISSN (Electronic): 2352-3409
                Publication date PMC-release: 14 March 2016
                Publication date Collection: June 2016
                Publication date (Electronic): 14 March 2016
                Volume: 7
                Pages: 747-750
                Affiliations
                [a ]Department of Pharmaceutical Sciences, College of Pharmacy, Byrd Alzheimer׳s Institute, University of South Florida-Health, 4001 E. Fletcher Ave, MDC36, Tampa, FL 33613, USA
                [b ]Florida Center of Excellence for Drug Discovery & Innovation at the University of South Florida, 3720 Spectrum Blvd., Suite 303, IDR Building, Tampa, FL 33612, USA
                Author notes
                [* ]Corresponding author. Tel.: +1 813 396 0673; fax: +1 813 905 8862. UJinwal@ 123456health.usf.edu
                Article
                Publisher ID: S2352-3409(16)30134-2
                DOI: 10.1016/j.dib.2016.03.026
                PMC ID: 4804223
                PubMed ID: 27054189
                SO-VID: 96b377c6-dc4e-4aca-bd31-084e1d05aa0e
                Copyright © © 2016 The Authors
                License:

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 25 November 2015
                Date revision received : 4 March 2016
                Date accepted : 4 March 2016
                Categories
                Subject: Data Article

                Keywords: withaferin a,microglial cell line,silac,proteomics,mass spectrometry
                Data availability:
                Keywords: withaferin a, microglial cell line, silac, proteomics, mass spectrometry

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