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Since most of the miRNAs used on the microarray are not present at detectable levels in most serum samples, clustering was only performed on a subset of the miRNAs.
Due to the presence of 11 different oligonucleotide sets for each specific gene being used on the microarray versus only a single primer set for a gene in a quantitative PCR, the microarray is more effective at eliminating false positive or negative data and provides a more robust quantification of changes in gene expression.
Due to the presence of 11 different oligonucleotide sets for each specific gene being used on the microarray versus only a single primer set for a gene in a quantative PCR, the microarray is more effective at eliminating false positive or negative data and provides a more robust quantitation of changes in gene expression.
These primers were designed independently from the oligonucleotides used on the microarray.
Cross-hybridization between the Cy3-labelled (cZIP on the) padlock probe and other ZIP-codes that were used on the microarray was not observed (results not shown).
Differences may reflect disparities between the probes used on the microarray platform, NanoString probes, and the primer sets employed for RT-PCR.
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RT-PCR analysis of the RNA samples used on the microarrays confirmed previous observations [3] that the expression of these genes is indeed reduced in embryos in which activin signalling is inhibited (data not shown).
The authors compared transcript levels in filaments and in a heterocyst-enriched fraction; the multi-gene features used on the microarrays limited the interpretation of the results.
We used S288C as the reference DNA since this is the strain that was sequenced and from which the PCR products used on the microarrays were generated; the Cy3-labeled DNA should thus give a green signal in every channel.
However, it is important to note that the cDNA probes used on the microarrays do not enable efficient differentiation between the aforementioned CYP members, which share a relatively high sequence homology.
The gene model used on this microarray included the 5' end of the coding sequence but was not predicted to be targeted to the plastid even though other plant ADPGp large subunits were.
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