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Amplified cRNA samples were used for microarray hybridization only if the yield is > 825 ng and the specific activity is > 8.0 pmol Cy3 or Cy5 per ug cRNA.
For microarray hybridization only male embryos were used and each condition was performed on at least three biological replicates from different litters except for E16 embryos for which two biological replicates were used.
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This change in the mRNA expression levels between F1 and ovulated oocytes is probably insufficient to be detected in the comparison between Ov GDR and F1 GDR by microarray hybridization, since only 7 differentially expressed genes were identified in this comparison.
We generated a subset of microarray hybridization signals containing only genes and ESTs with higher expression in dormancy-released flower buds (flower-bud late genes) according to previous works [ 24, 25].
However, obtaining data of gene expression via sequencing rather than using specific microarray hybridization would not only allow detection of novel transcripts and retrieve species-specific data, but would reduce bias in gene expression profiling from possible cross-species hybridization mismatches [ 16, 18, 19].
Studies based on cDNA library analysis and microarray hybridization have shown that only a subset of the mouse OR gene repertoire is expressed at detectable levels in the olfactory epithelium [ 9, 27].
To discriminate between these two possibilities, we performed a dye-flip microarray hybridization experiment using samples differing only in the presence or absence of added amplicons of known HS genes represented on the array.
Total RNA of RFP-negative cell populations were only collected and used for qRT-PCR verification, but not in microarray hybridization.
This model considers hybridization only on one spot on the microarray.
Our main results are the scatterplot showing microarray hybridization signals using a probe derived from muscle mRNA, versus the signals using only an oligo dT) probe (Fig. 2).
Only RNA samples with an A260/A280 ratio > 1.8 were used for microarray hybridization.
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