map3k8 br Experimental design The dataset presented here was

Experimental design The dataset presented here was obtained from using the label-free proteomic analysis of three different strains of Prototheca species, P. zopfii genotype 1, genotype 2 and P. blaschkeae representing non-infectious, infectious and moderately infectious strains, respectively. In total 17 samples representing six independent cultures for each (only five in P. zopfii genotype 2) were used to generate the dataset (experimental design is shown in Fig. 1). A Student-t test, p-value <0.05% and 1% false discovery rate (FDR) was applied for identification of differentially expressed proteins between (a) P. zopfii genotype 2 and P. zopfii genotype 1; (b) P. blaschkeae and P. zopfii genotype 1; and (c) P. zopfii genotype 2 and P. blaschkeae.
Materials and methods
Acknowledgements We would like to thank Michael Kühl for excellent technical assistance. We acknowledge the assistance of the Bio-MS unit of the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). The author Murat Eravci was supported by the Deutsche Forschungsgemeinschaft (DFG, SFB958). We thank the PRIDE team for their assistance in the MS data deposition.
Data The data exhibited the average water consumption of each DM mouse administrated with PGPSD polysaccharide or metformin hydrochloride for consecutive days. The daily water consumption of each group with different treatments was shown in Fig. 1.
Experimental design, materials and methods
Funding sources This study was supported by the National Natural Science Foundation of China (No. 31272120) and the China Agriculture Research System (No. CARS-31).
Acknowledgements
Data Thyme leaf metabolites are presented in two map3k8 of polar and non-polar metabolites. M/z value of metabolites ranged 70–590 m/z for polar fraction and 70–2000 m/z for non-polar fraction of extracted samples. Peak intensities in control (watered) and droughted grown plants are presented in the tables. T-test was used to identify the significant differences between the watered and droughted metabolites [1].
Experimental design, materials and methods Thymus vulgaris and Thymus serpyllum (as representative of drought sensitive and drought tolerant plants respectively) were grown in a growth room with a 16:8 (light: dark) cycle and a temperature of 22°C and watered with tap water weekly. Drought stress was applied as described previously [4]. Similar aged leaves of six individual plants as biological replicates were harvested for FTICR profiling at the end of drought stress period (Fig. S1). Freeze dried samples were extracted using the methanol: chloroform: water protocol and separated extracts to polar and non-polar fractions. Polar extracts were dried with a vacuum concentrator (Thermo Savant, Holbrook, NY, USA) and non-polar extracts were dried under a stream of dried nitrogen gas. The dried extracts were stored at −70°C until analysis. Three technical replicates containing 10µl aliquots from each polar and non-polar samples were analyzed using a hybrid 7-T Fourier Transformed Ion Cyclotron Resonance Mass Spectrometer (LTQ FT, Thermo Scientific, Bremen, Germany) equipped with a chip-based direct infusion nanoelectrospray ionisation assembly (Triversa, Advion Biosciences, Ithaca, NY). ChipSoft software (version 8.1.0, Advion Biosciences) was controlling the Nanoelectrospray conditions which had 200nL/min flow rate, 0.3psi backing pressure, and +1.7kV electrospray voltage for positive ion analysis and −1.7kV for negative ions.
Acknowledgements I appreciate Dr. Jennifer Kirwan, Professor Mark Viant and Dr. William Allwood, Ralf Weber for their help regarding the experimental design in metabolomics investigations. I would like to thank Islamic Development Bank (Scholarship file No.30/IRN/P30) (IDB) and my home institute (Iran) for generously providing comprehensive financial funding for my Ph.D. program.
Data We investigated the effects of alkaline pH on the proliferation of developing osteoblasts of the osteoblast-like cell line MC3T3-E1. Cell count, cellular WST-1 metabolism, and ATP content were analyzed. The three parameters showed a pH optimum around pH 8.4 [1]. Here we present details of the tests that were carried out to verify the WST data. The first test was performed to exclude a possible pH effect on the photometric measurements (Fig. 1, and Supplementary file 1). The second test was performed to evaluate the pH-dependence of the mitochondrial succinate reductase, which metabolizes the WST-1 reagent (Fig. 2, and Supplementary file 2). The third test was conducted to analyze possible changes of the pH dependence over the culturing period of six days (Fig. 3, and Supplementary file 3).