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To test the validity of signal quantitation by the Pinus microarray, 60-mer probes were selected and corresponding transcripts in cDNA transcribed from the original total RNA extracts used for microarray hybridisation were quantified by RT-PCR.
The 14 samples from the hippocampus used for microarray hybridisation were also analyzed by qPCR analysis.
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These qPCR experiments were carried out on the same pools used for microarray hybridisations.
Leaf material was used for microarray analyses.
The cDNA used for the microarray hybridisation was first diluted 10-fold.
In brief, total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) and used for target preparation for microarray hybridisation.
To assess the impact of the additional T7 nucleotide sequence on the specificity of the ADP primers, 5 μg M. tuberculosis H37Rv RNA was labelled for microarray hybridisation using reverse transcriptase with 2 μM ADP primer +/- the 5' anchor, T7 polymerase binding sequence, and random four nucleotide sequence.
To obtain RNA for microarray hybridisation, we used the following procedure.
To generate fluorescently labelled samples for microarray hybridisation, we used a direct labelling protocol.
For microarray hybridisation we used a common reference design as proposed by Dudley et al. [ 68], in which a fluorescence labelled antisense oligonucleotide (complementary to a sequence tag present in all spotted microarray probes) is hybridised together with the labelled cDNA of interest.
It is also cost effective when compared with methods using multiple column steps, and provides labelled targets for microarray hybridisation with an optimal coefficient of repeatability.
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