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Each time-point (6, 12, 24, 48 h) and sham-operated (sh) group consisted three animals per group; RNAs from each individual were separately labelled and analyzed by microarray hybridization, for a total of 15 microarray hybridizations.
Expression data produced by microarray hybridization for 79 developmental stages of A. thaliana were downloaded from EBI ArrayExpress (accession number E-AFMX-9, [ 18]) and expression profiles were compared with expression profiles obtained by LongSAGE for B. napus seeds using hierarchical cluster analysis and Spearman's rank correlations according to Lu et al. [ 19].
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Plasmid-encoded genes involved in conjugation and mobilization as well as replication and maintenance were assessed by microarray hybridization analyses or, for a few targets, by PCR (Additional file 3: Figures S2A and Additional 5: Figure S3A).
Mean values of fold difference for each cohort were compared to mean values obtained for pools analyzed by microarray hybridization.
Analyzing MuHV-4 lytic transcripts by microarray hybridization [9] [11] has been of limited use for ORFs 75a/b/c, because latency associated ORF73 mRNAs splice across them [12].
Changes detected by microarray hybridization were confirmed by real time PCR for Acly, Kat2a, Dhx28, and Stat5a (data not shown).
Thus, PCR analysis confirmed the results for RA versus ND as determined by microarray hybridization.
The samples were analyzed by microarray hybridization and quantitative PCR.
To summarize, through this first compilation of putative sRNA-encoding IgRs, we obtained experimental evidence by Northern and/or microarray hybridization for eight novel S. meliloti RNA transcripts corresponding to candidates IgR 2, IgR 6, IgR 7, IgR#11, IgR#15, IgR 16, IgR#17 and IgR 18 (Table 1, Figure 1).
We began by comparing results obtained using sscDNA and cRNA microarray hybridizations for all 12,625 probe sets on the arrays.
We began by analyzing the transcipt length measurements derived from microarray hybridization data for the 1,236 cDNA clones that map to more than one Unigene cluster.
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