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The microarray protocol used in the present study proved to be both reliable and repeatable.
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Most microarray protocols use mRNA amplification, which also results in amplification of coronavirus RNAs.
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit.
Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).
For mRNA expression, samples were prepared according to the Agilent mRNA Microarray System protocol using 250 ng of total RNA for amplification and labelled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit.
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies) and Agilent's recommended hybridization chamber and oven.
The methods were the padlock probe ligation in combination with microarray detection (PPLMD I) [ 8], another padlock probe approach also combined with microarray detection (PPLMD II) [ 10], the protocol used in the dual tag microarray method (DTM) [ 17], a ligation-dependent probe amplification (LPA) protocol [ 12] and the SNPlex approach as described by Chaouachi et al. [ 15].
A comprehensive understanding of the experimental protocol used in a microarray experiment aids the interpretation of the obtained results.
In this article we describe the experimental protocol used for Affymetrix microarrays and important factors that may influence its outcomes, summarized in Fig. 5.
Each centre is trained on an identical microarray protocol and uses the same equipment and kits for target preparation (Affymetrix HG-U133 Plus 2.0).
Protocol used for preparation of RNA and hybridization for microarray has been previously described [31].
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