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This "Catch-3" step is analogous to the DNA microarray hybridization step in the proteomics assay.
Moreover, we demonstrate that they result from large and continuous spatial biases on the microarray surface, which are generated at the microarray hybridization step.
Using computer simulations, we show that large spatial biases caused in the microarray hybridization step and independently of printing procedures can exclusively account for the observed spurious correlations, in contrast to previous suggestions.
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Microarray hybridization and washing steps were performed following the Agilent protocol for single-channel arrays.
The optimization of the microarray workflow, including the hybridization step, is thus a primary target for the evolution of more efficient protocols.
The two-step microarray hybridization was carried out with the 3DNA 50 Expression kit (Genisphere Inc., Hatfield, PA).
Total RNA samples were aliquoted (20 μg each) for cDNA synthesis and 2-step microarray hybridization with 3DNA 50 Expression kit (Genisphere Inc., Hatfield, PA).
Both mixed sample and microarray were kept at 55°C until the hybridization step.
A polyA-based priming step in many labeling protocols for microarray hybridization is an example: It leads to a considerable 3' bias [ 29].
To avoid systematic bias due to batch/lot and processing variability, bariatric surgery samples and control samples were balanced and randomized in each of the following steps: adipose tissue homogenization, RNA extraction, labeling, and microarray hybridization.
All steps of microarray processing (cDNA production, cDNA labeling, microarray hybridization, data quantification, data normalization using LOWESS) were carried out by the TIGR Expression Profiling Service [ 15].
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