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  • br Data In order to inform the SPIDIA DNA

    2018-10-25


    Data In order to inform the SPIDIA-DNA EQA participants on the quality of the extracted DNA from blood a dedicated report was realized [1,4]. The report contains the evaluation of the performance of the specific laboratory and the overall distribution of the participants’ data for each gDNA quality parameter.
    Experimental design, materials and methods Briefly, 1.2ml of blood from a single healthy donor was sent to 174 laboratories from 26 different European countries (Fig. 1). The participants extracted gDNA following their own procedure within 3 days from blood arrival, performed the spectrophotometric measurements and shipped back the sample at 4°C. At SPIDIA facility, the defined DNA quality parameters (DNA purity and yield, gDNA integrity and of qPCR interferences) were evaluated and the performance of each laboratory was defined. A specific report (Appendix A, Supplementary material) was realized to give to the participants: (I) their own performance evaluation for each gDNA quality parameter; (II) the overall performance evaluation of the whole exercise and (III) the overall data distribution for each parameter.
    Specifications Table Value of the data Data Agmatine and glutamic Senexin B have a different effect on the phenotype of F. graminearum[1] that is also reflected in shared proteomic profiles discussed in [1]. Here we detail the complete list of all identified proteins that change significantly among strains or between conditions for each strain. In the list of protein species that are significantly shifting their abundance in each of the three strains representing F. graminearum toxigenic variability (Supplementary material 38) proteomic profiles for each strain can be obtained. By selecting the protein species with opposite behaviour among the strains we identified a subset of proteins that can be used to discriminate the three strains used here (Fig. 1). This dataset is also useful for comparing how different strains behave at the proteomic level when grown in agmatine or glutamic acid as the sole nitrogen source.
    Experimental design, materials and methods
    Specifications Table
    Value of the data
    Data The images shown here consist of raw microscope images (left) and software-binarized images (right) acquired or generated for individual cell culture experiments in the associated primary research article [1]. The first image acquired for each treatment group is shown; please refer to the Supplementary materials for the full set of raw microscope images. The information included above (i.e. specifications table, value of the data, data description in this paragraph) applies to all image sets below. Experimental design, materials and methods are included in both general and experiment-specific terms.
    Experimental design, materials and methods
    Experiment 1: baseline cell line characteristics This experiment investigated baseline mitochondrial network characteristics of GK vSMCs, Wistar vSMCs, HUVECs, and SH-SY5Ys. See Fig. 1.
    Experiment 2: effects of fixation temperature in HUVEC cells HUVEC cells were cultured without experimental perturbation for 6–10 passages. Cells were divided into one of four experimental groups and fixed according to the protocol described above. Group 1 was fixed using reagents pre-heated to 37°C and all incubation steps during fixation were performed at 37°C; Group 2 was fixed using room-temperature reagents and all incubation steps during fixation were performed at 37°C; Group 3 was fixed using room-temperature reagents and all incubation steps during fixation were performed at room temperature; Group 4 was fixed using reagents pre-heated to 37°C and all incubation steps during fixation were performed at room temperature. See Fig. 2.
    Experiment 3: high glucose exposure with primary rat SMCs Primary smooth muscle cells from the aorta of GK or Wistar rats were cultured in low glucose (5mM) smooth muscle growth media until passages 8–10. Prior to treatment, cells were switched to low glucose, serum free starvation media for 48h. Serum starved cells were exposed to high glucose (25mM), serum free media. For each cell type (GK and Wistar) in each repetition of each experiment, 15 slides were prepared. Of these 15 slides, three were merely rinsed with high glucose media before fixation and staining (0min exposure), three were fixed and stained after 10min in high glucose media, three were fixed and stained after 30min in high glucose media, three were fixed and stained after 30min in high glucose media, three were fixed and stained after 60min in high glucose media, and the remaining three were fixed and stained after 240min in high glucose media. See Figs. 3 (GK) and 4 (Wistar).