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Starting total RNA yields were not sufficient for microarray hybridizations due to the small amount of caudal fin tissue present on these young fish.
Pacing-induced alterations in the expression of other miRNAs with particular concern for their involvement in AF could not be determined by microarray hybridizations due to a high variability among replicates (miR-1, miR-21, miR-23a/b, miR-29a, and miR-133a) or very low hybridization signals (miR-10a, miR-10b; see the complete microarray data at NCBI through GEO accession number GSE65330).
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To exclude the possibility that the low LPI values of these could have resulted from the loss of signal in microarray hybridization due to sequence variability in the gene, we examined the OthoMCL output of all sequenced genomes in this analysis.
Some of the selected negative cDNA clones may have produced a weakly positive signal in northern or microarray hybridization experiments due to fairly small stretches of sequence similarity to transcripts present in glucose-grown fungus resulting in cross-hybridization.
Due to the nature of microarray hybridizations, which are much like the interpretations of Southern blot data [ 24], only a positive hybridization can reliably be interpreted.
Such regions would be unsuitable for nucleosome position analysis by microarray, because differential hybridization due to nucleosome association could not be distinguished from differential hybridization due to genetic differences.
For each plasmid, we performed three transfections and three microarray hybridizations.
Microarray hybridizations were performed in triplicates for each strain.
Microarray hybridizations were performed on the 22K Agilent platform.
cDNA microarray hybridizations.
JK performed the microarray hybridizations.
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