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Duplicate samples were analyzed in duplicate microarrays, and data were further analyzed by VAMPIRE and GeneSpring.
Each case pool was assayed on duplicate microarrays.
Each of the spiked pools was assessed on duplicate microarrays.
Each polyp was analyzed with duplicate microarrays on each occasion.
The perfect alignment of signals detected for these spikes along the line of identity on plots comparing duplicate microarrays validates the technical reproducibility of the data (not shown).
Specifically, we first compared gene expression in wild type cells grown in low and high zinc and identified 458 genes expressed more highly in low zinc in duplicate microarrays.
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We averaged the ratios from duplicate microarray hybridizations and used the same threshold as for HeLa cells to define the target promoters occupied by Myc in foreskin fibroblasts.
In the present study, we further characterized one of the EST transcripts (GenBank accession # R13346) which was induced by EWS/WT1 −KTS) expression with variable magnitudes in duplicate microarray experiments (21.0- and 3.1-fold induction).
These results showed the consistency of our duplicate microarray experiments.
Briefly, a twofold difference was considered significant if three criteria were met: (1) the GeneChip software returned a difference call of increased or decreased; (2) the mRNA was called present by GeneChip software in either germ-free or conventional samples; and (3) the difference was observed in duplicate microarray experiments.
Total RNA from each culture was isolated, converted to fluorescently labeled cDNA, and hybridized in duplicate to microarrays.
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