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The microarray assays were carried out by Takara Bio. Inc. (Otsu, Japan) using products for microarray analysis manufactured by Agilent Technologies, according to the manufacturer's protocols.
Another possible explanation for the inhibitory effects of S-PRG eluate on the in vitro cariogenic properties of S. mutans is that the S-PRG eluate may affect other S. mutans virulence genes since DNA microarray assays were performed under fixed incubation conditions.
Genes showing differential expression in the microarray assays were determined by setting the number of falsely called genes to less than one for the significant gene list output.
Microarray assays were performed on a μParaFlo microfluidics chip with each of the detection probes containing a nucleotide sequence of coding segment complementary to a specific candidate miRNA sequence.
Gene expression microarray assays were performed in quadruplicate for each patient and 16 out of the 20 chips were selected on the basis of standard quality metrics and uniformity of hybridization.
Microarray assays were performed on a μParaFlo microfluidics chip with each of the detection probes containing a nucleotide sequence having a coding segment complementary to a specific candidate miRNA sequence in order to confirm its existence in the silkworm.
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All of the samples for the regular cDNA microarray or SSH/microarray assays were performed with the dye-swapping microarray design for minimizing labeling bias and statistical variances of data.
TaqMan assays were run for 48 genes on each of the 5 RNA samples that were used in microarray and RNA-seq assays.
Selected cDNA microarray observations were confirmed by RNase protection assay.
Microarray chips were scanned using a DNA Microarray Scanner (Agilent Technologies).
Microarray experiments were conducted according to the manufacturer's instructions.
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