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Softmax pro v 7.03

Manufactured by Molecular Devices

SoftMax Pro (v.7.03) is a microplate reader control and analysis software. It provides data acquisition and analysis capabilities for various microplate-based assays.

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4 protocols using softmax pro v 7.03

1

Metabolomics Data Analysis Pipeline

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Metabolomics data analysis, including log2 transformation, quantile normalization and Pearson’s correlation with p-value calculation and false discovery rate-adjusted q-value calculation, was performed using an in-house R package (https://github.com/kuppal2/xmsPANDA). We selected q<0.25 for multiple comparisons adjustment of metabolomics results due to the convolution inherent to electrospray ionization mass spectra (multiple signals can be observed per compound). Additional analysis was performed using MetaboAnalyst (15 (link)) and ggplot2 (16 (link)). MPO assays were calibrated by SoftMax Pro v. 7.0.3 (Molecular Devices). Prism 7 (GraphPad) was used to calculate Spearman correlations and Mann-Whitney U test, and to generate figures.
Additional methods are located in the Supplementary Information document accompanying this manuscript.
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2

NanoBiT β-Arrestin Recruitment Assay for PTH1R

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β-arrestin recruitment to PTH1R was measured using the NanoBiT β-arrestin-recruitment assay52 (link) with minor modifications. In brief, plasmid transfection was performed in a 6-cm culture dish with a mixture of 200 ng N-terminal large BiT-fused β-arrestin 1 (Lg-β-arrestin 1) or Lg-β-arrestin 2 and 1,000 ng C-terminal small BiT-fused PTH1R (PTH1R-Sm) plasmids. After 24 h of incubation, the transfected cells were collected using 0.53 mM EDTA-containing D-PBS, centrifuged at 190g for 5 min and suspended in 4 ml of the assay buffer described for the GloSensor assay. The cell suspension was dispensed into a white 96-well plate at a volume of 80 μl per well (hereafter 96-well plate) and loaded with 20 μl of 50 μM coelenterazine (Carbosynth) diluted in the assay buffer. After 2 h of incubation at room temperature, the plate was measured for baseline luminescence (SpectraMax L equipped with 2PMT, Molecular Devices; SoftMax Pro (v.7.03), Molecular Devices) and 20 μl of 6× ligand diluted in the assay buffer or vehicle was manually added. The plate was read for 15 min with a 40 s interval at room temperature. The luminescence counts from 13 to 15 min after ligand addition were averaged and normalized to the initial counts.  the response were fitted to all data using the same procedure as described for the GloSensor assay.
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3

NanoBiT β-Arrestin Recruitment Assay for PTH1R

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β-arrestin recruitment to PTH1R was measured using the NanoBiT β-arrestin-recruitment assay52 (link) with minor modifications. In brief, plasmid transfection was performed in a 6-cm culture dish with a mixture of 200 ng N-terminal large BiT-fused β-arrestin 1 (Lg-β-arrestin 1) or Lg-β-arrestin 2 and 1,000 ng C-terminal small BiT-fused PTH1R (PTH1R-Sm) plasmids. After 24 h of incubation, the transfected cells were collected using 0.53 mM EDTA-containing D-PBS, centrifuged at 190g for 5 min and suspended in 4 ml of the assay buffer described for the GloSensor assay. The cell suspension was dispensed into a white 96-well plate at a volume of 80 μl per well (hereafter 96-well plate) and loaded with 20 μl of 50 μM coelenterazine (Carbosynth) diluted in the assay buffer. After 2 h of incubation at room temperature, the plate was measured for baseline luminescence (SpectraMax L equipped with 2PMT, Molecular Devices; SoftMax Pro (v.7.03), Molecular Devices) and 20 μl of 6× ligand diluted in the assay buffer or vehicle was manually added. The plate was read for 15 min with a 40 s interval at room temperature. The luminescence counts from 13 to 15 min after ligand addition were averaged and normalized to the initial counts.  the response were fitted to all data using the same procedure as described for the GloSensor assay.
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4

Luminol-based Leaf Disc ROS Assay

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Leaf discs (4 mm in diameter) were taken from the center of leaves from plants of various ages and floated with abaxial side down in wells of a white 96-well plate containing 200 μl sterile water in each well. Plates were covered with foil and leaf discs were kept in sterile water overnight to attenuate wounding response. After 24 h, water was removed from wells and replaced with 100 μl of an immune-eliciting solution containing 34 μg ml−1 luminol (Sigma, A8511), 20 μg ml−1 horseradish peroxidase (Sigma, P6782) and 100–250 nM of the indicated PAMP/DAMP. Luminescence measurements were collected (total photon counting) over 40 min immediately after the addition of immune-eliciting solution using a SpectraMax L microplate reader with SoftMax Pro v.7.0.3 (Molecular Devices). Total ROS was calculated for each sample in Prism v.10.0.0 (GraphPad) using the ‘Area under curve’ analysis.
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