br Acknowledgments We thank Sofie Vande Casteele for the

Acknowledgments We thank Sofie Vande Casteele for the assistance with the maintenance of our Waters Premier LC–MS, the platform applied for the development, and optimization of the protocol. We thank Niklaas Colaert for the support with the Rover software and Kristof De Beuf from the FIRE Statistical Consulting of the Ghent University for the help with the statistics. For the LC–MS acquisitions of the final samples, we acknowledge Ernst Bouvin and Christian Baumann from ABSciex; Hans Vissers, Chris Hughes, and Jan Claereboudt from the Waters Corporation; and Wilfried Voorhorst and Heike Schaefer from Thermo Fisher Scientific. We also thank the PRIDE team for creating a platform to share our data publically. This research is funded by a Grant from the Fund of Scientific Research Flanders (FWO: 3G073112) and a Ph.D. Grant (SB-11179) from the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) awarded to P.M. D.D. and L.M. acknowledge the support of Ghent University (Multidisciplinary Research Partnership “Bioinformatics: from nucleotides to networks”). L.M. also acknowledges support from the PRIME-XS project funded by the European Union Seventh Framework Program under Grant Agreement no. 262067.
Specifications table Value of the data Data, experimental design, materials and methods
Acknowledgements KZ thanks the funding support from University of Illinois at Urbana-Champaign (UIUC), United States. We thank Prof. Joseph Gall at the Carnegie Institution for Science for providing the pCRII plasmid and Prof. XL Nan in the Oregon Health and Science University for providing the ERK-GFP plasmid. We thank Dr. Sandra McMasters from the cell media facility of UIUC for providing DH5α competent purchase Deforolimus and for her insightful comments on our experiments.
Value of the data Experimental design Valuable information about the proteome changes in the longissimus thoracis (LT) bovine muscle in response to pre-slaughter stress (PSS) was obtained from 2-DE data. The occurrence of Dark, Firm and Dry (DFD) meat was used as indicator of animals affected by PSS. A total of four biological replicates of control (normal or non-DFD) and DFD meats from male calves of the Rubia Gallega breed (Spain) were used in this study. DFD and control samples were selected from 76 male calves after evaluation of meat quality parameters that differentiate both types of meat [1]. 2-DE protein spots with statistically significant changes in protein abundance between control and DFD samples were identified by mass spectrometry (MS).
Materials and methods
Value of the data
Data, experimental design, materials and methods
Conflict of interest
Specifications table Value of the data Data, experimental design, materials and methods
Acknowledgments We thank the Pride Team (http://www.ebi.ac.uk/services/teams/pride) for assistance with MS data deposition. This work was supported in part by United States National Science Foundation EAGER Grant MCB-1355462 and the Zegar Family Foundation Fund for Genomics Research at New York University.
Specifications table
Value of the data
Data, materials and methods MIC26 depletion induces a number of physiological impairments in mitochondria including a decrease in respiration and an altered mitochondrial ultrastructure [1]. Here we show data to demonstrate that the miRNA used in Koob et al. is specific to MIC26. For that a miRNA-resistant form of N-terminal myc-tagged MIC26 was used. Fig. 1A shows that expression of the conventional myc-MIC26 construct in MIC26↓ cells resulted in a decrease of myc-MIC26 and endogenous MIC26 levels. Likewise, protein levels of MIC27 were increased and those of MIC10 were decreased as reported before [1]. When the miRNA-resistant form was expressed in cells constitutively downregulated for MIC26 protein levels of myc-MIC26 were not reduced demonstrating that the expressed miRNA does not target these particular myc-MIC26 transcripts. Moreover, MIC26 specific effects on MIC27 or MIC10 were not observed using the miRNA resistant myc-MIC26 construct (Fig. 1A).