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This resulted in Mock corrected Log2 ratio values for every microarray, including the Mock arrays.
For this study, a total of 102 SNPs were detected by the microarray, including the 22 missense mutations considered to be pathogenic (Table 3).
Only a few known GA signaling genes were identified as HSR in our microarray, including the GA receptor, GID1A, and signaling components such as SPY and SLY.
For this study, a new version of Manila clam DNA microarray including the sequences of thousands of hemocyte-exclusive genes [ 21] was designed and developed.
This provides an opportunity to examine the utility of the three sets of ORF features on the GMAP microarray, including the 22-mer hairpin features designed to detect shRNA barcodes.
Additional file 1 shows functional annotation of the genes represented in the microarray, including the ID, description and E value of the first BLAST hit from the databases used for annotation (UniRef90 [ 22] and Arabidopsis TAIR full set of proteins [ 23]), as well as their Gene Ontology classification [ 24] and pfam domains [ 25].
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The output files from each microarray include the signal (MedianSignal), standard deviation of the signal (PixSDev), background (BGMedianSignal), and corrected signal (ProcessedSignal -dye-normalized surrogateter surrogalgorithmithm, used for computation of ratio values) for each channel.
Each microarray included the probes described in Table 1: QC1, and QC11, the complementary sequences to which were included in the hybridization solution at a concentration of 100 pM.
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.
The L. interrogans strain Lai microarray included the 7 genes coding for hemolysins [ 36, 37], of which, 5 (LA0327, LA0378, LA1650, LA3050 and LA3937) were conserved among all strains tested.
We show that the predicted HLH-25 transcriptional network, based on gene expression microarray, includes the Pten ortholog DAF-18 and other genes that mediate cell division, embryonic development, and larval development.
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