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Prism 5 program

Manufactured by GraphPad
Sourced in United States

Prism 5 is a data analysis and graphing software program developed by GraphPad. The software is designed to help users analyze, visualize, and present their data in a clear and effective manner.

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6 protocols using prism 5 program

1

Survival Analysis of Treatment Outcomes

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Kaplan-Meier survival curves were compared with the log-rank test using the Prism 5 Program(Graph Pad, San Diego, CA). A p-value < 0.05 was considered significant.
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2

Triplicate Biological Assay Analysis

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All experiments were performed at least in triplicates. Data were analyzed using the Prism 5 Program (Graph Pad, San Diego, CA, USA). Values are presented with individual data points + mean. Statistical difference was determined by one-way ANOVA followed by Tukey’s range test. A P-value of <0.05 was regarded statistically significant.
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3

Purification and Spectroscopic Analysis of Fluorescent Protein Fusions

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E. coli BL21(DE3) cells carrying pET derivative plasmids were grown at 37 °C in Lysogeny Broth to an OD600 of 0.5, and gene expression was induced by the addition of 100 µM IPTG for 12 h at 17 °C. Proteins were purified by immobilized metal ion chromatography as previously described [35 (link)]. Spectroscopic analyses were monitored in 96-well plates using a TECAN Infinite®® 200 series microplate reader (Hännedorf, Switzerland) equipped with a dual injector head for kinetic measurements. The excitation and emission bandwidths of the instrument are 9 nm and 20 nm, respectively. For in vitro and in vivo experiments, fluorescence emissions were recorded using an excitation at 425 nm, and emissions at 530 nm and 480 nm for YFP and CFP, respectively. The FRET ratio was calculated as the 530/480 intensity ratio (YFPem/CFPem) and reflects the level of excitation of YFP by the CFP, which is directly linked to the distance between the two fluorophores. The relative FRET ratio was calculated as the FRET ratio for a specific 2-OG concentration relative to the same ratio without 2-OG. The data were analyzed by the PRISM 5 program (GraphPad Software, San Diego, CA, USA). For in vitro experiments, fluorescence emissions were recorded 5 min after ligand addition.
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4

Fluorescence Polarization Assay for PadR DNA Binding

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A fluorescence polarization (FP) assay was performed to determine the dsDNA-binding affinity of wild-type (WT) and mutant PadR (37 (link)). The PadR proteins were prepared by dialyzing against FP assay buffer containing 20 mM Tris, pH 8.0 and 100 mM NaCl. The dsDNA was generated by incubating a fluorescein-labeled oligonucleotide (5′-C1GGAACATGTAAATAGTTACATGATTAC28-3′) and its unlabeled complementary counterpart (5′-G1TAATCATGTAACTATTTACATGTTCCG28-3′) at 95°C for 5 min and then slowly cooling the reaction to the room temperature. The dsDNA (1 nM) was incubated with serially diluted PadR dimer (PadRdimer) protein (0.6 nM–4 μM) in the FP assay buffer in 96-well plates (Corning). The FP signals were measured using an Infinite F200 PRO instrument (Tecan; excitation wavelength, 485 nm; emission wavelength, 535 nm) and analyzed using the Prism 5 program (GraphPad).
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5

Adipocyte Isolation and Characterization

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A critical factor in the development of this procedure was to keep track of all weights/volumes and incorporate into the calculations all aliquots extracted for testing (i.e., glucose or lactate levels). All data were introduced in a spreadsheet in which the volumes were justified with a (pipetting) error of ±3%. When possible, or when no other avenue was available, volumes were estimated from differential weights and the application of the densities calculated as described above.
The calculations used to determine the cell parameters, adipocyte recovery and WAT cell distribution are described in the Tables, presenting the original experimental data along with the derived or calculated data, as well as the formulas used for their estimation.
Statistical analyses were carried out using the Prism 5 Program (Graphpad Software Inc., La Jolla, CA, USA). Statistical differences between groups of data were determined with the unpaired Student’s t test.
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6

Triplicate Assay Method Validation

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All the experiments were performed three times in triplicates. Data were presented as mean ± standard deviation. Statistical analysis was performed using GraphPad Prism 5 Program (San Diego, CA, USA). One-way ANOVA test was applied followed by Bonferroni's multiple comparison test to determine the significance.
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