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The viability of the reporter bacterium was determined by a fluorescence live/dead cell staining method and visualized by confocal laser scanning microscopic observation.
The eluted chromatography fractions were then quantified in a spectrophotometer with Bradford's method and visualized by SDS-PAGE (Laemmli 1970).
Clustering was done using Gene Cluster version 3.0, using the "centered" Pearson correlation similarity metric and complete linkage clustering method, and visualized using Java TreeView.
A phylogenetic tree was made using Bootstrap neighbour-joining method and visualized by NJPlot.
Clustering was conducted using Ward's minimum variance method and visualized with clustered image maps (heatmaps).
The sequence similarity of 89 TEs was analyzed by the hierarchical clustering method and visualized with help of multidimensional scaling.
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EGFP labeling was enhanced by staining with a GFP antibody (Online Methods) and visualized by an AlexaFluor-488-conjugated secondary antibody.
Proteins from 6 × 108 cell equivalents were resolved by one-dimensional SDS PAGE (using standard protocols) and two-dimensional SDS PAGE (see Supplementary Methods) and visualized by staining with Coomassie blue.
Northern blotting and hybridization were performed according to standard methods and visualized with the AlkPhos Direct™ Labeling and Detection System (Amersham Biosciences).
Differentially expressed genes were hyperclustered (see Materials and Methods) and visualized using the pooled gene list.
Peroxidase activity was detected by using chemiluminescence method (Amersham) and visualized on X-Omat S films (Amersham).
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