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The washed beads were used for loading gels and immunoblot analysis.
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Supernatant was collected and quantified with 2-D Quant Kit (Amersham Biosciences) before loading gels for 2D-DIGE separation.
To check for loading, siRNA gels were cut above the xylene cyanol band and stained with ethidium bromide.
From each serum sample, 25 μl was taken to be mixed with 200 μl (for LDL, IDL and VLDL) or 300 μl (for HDL) of LipoPrint loading gel and loaded on the upper part of the 3 % polyacrylamide gel.
To compensate for subtle differences in sample loading, gel staining, and destaining, the volume of each spot (i.e. spot abundance) was normalized as a relative volume.
This is consistent with the difference in the amount of proteins used for loading 2-DE gels depending on the dye used afterwards, much smaller for silver-stained gels (100 μg) and the different dynamic range for each staining procedures [ 34].
Enzyme solutions (2×; 1.5 μM) were prepared in assay buffer 1 [AB1; 20 mM Hepes (pH 7.2), 10 mM MgCl2 and 0.01% Tween 20] and mixed with equal volumes of either (i) 200 μM ATP and 200 μM Axltide peptide substrate (KKSRGDYMTMQIG) in AB1 for loading into PAGE gels, or (ii) 200 μM ATP (with 1.5 μCi of [γ-P]ATP) and 200 μM peptide substrate in AB1 for RFB (radiometric filter binding) assays.
DNA is not yet ready for loading onto a gel.
Protein concentrations in fractions were determined using a bicinchoninic acid (BCA) protein assay kit (Pierce) and diluted for equal loading on gels.
A 2 mm channel was punched in the center of gel for loading the fluorescence dye as a diffusion source.
Orange DNA Loading Dye (Fermentas) was used for loading samples on agarose gel whereas O'GeneRuler 1 kb Plus DNA Ladder (Fermentas) was applied for sizing and quantification of DNA fragments.
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