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Production of Cy5-labelled and Cy3-labelled cDNA from the purified mRNA, hybridisation of the UniGEMV cDNA microarrays and quantification of the signals were performed by Incyte Genomics (Mountain View, CA, USA) as described previously [ 32].
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Microarray images and quantification data were then imported into GeneTraffic DUO (Stratagene, La Jolla, CA) for analysis.
Microarray detection and quantification should therefore allow the simultaneous measurement of copy number at a larger number of loci.
Raw microarray images and quantifications were stored and processed in Bio Array Software Environment BASEE, Lund Sweden) [ 13].
For example, the relative ranking based on the magnitude of fold differences, as predicted by microarray and qPCR quantification, is in general agreement within and between the two groups of candidate genes.
To optimize the dynamic range of microarrays and allow the quantification of both high and low copy expressed genes, the same arrays were scanned using different photomultiplier settings allowing selection of images with saturated image intensities on the 50 and 100 μM EC spots and on oligonucleotide spots for high-abundance genes such as Rpl5.
A possible source of higher variation relative to the reconstitution experiments was that microarrays and FACS based quantification were run on the same individual, but on different preparations of the bulk tissue such that variation in the cellular composition of the sectioned tissue per individual may have added to the experimental noise.
Genome-wide expression assays using DNA microarrays allow rapid screening and quantification of differences in large groups of functionally related genes and are thus well-suited to studies of pathways dysregulated in obesity [ 52].
Irrespective of whether the transcripts were rare (Gs and Pdk4) or abundant (Pepck and UbC), their changes in expression were similar in the microarray and qPCR quantifications.
The microarray Nylon cDNA hybridization and quantification using BZScan were the same as in [ 57].
The design specificities and goals of alternative splicing microarrays, in terms of identification and quantification of multiple mRNAs from one gene, are promoting the development of novel methods of analysis.
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