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For each time point, RNA from 5 mice was pooled and hybridized in quadruplicates, using a dye swap design to produce 4 expression measurements per time point.
Each experiment was performed in duplicate (technical replicate) using a dye swap design in order to account for dye biases.
Each experiment was performed in duplicate using a dye swap procedure and only the genes that independently complied with these filters on both replicates were considered.
Each of the 6 replicates was hybridized using a dye swap protocol resulting in 12 slides per group and 48 slides in total.
Hence, using a dye swap strategy, six arrays were hybridized using aRNA from replicates of 10 000 cells as a reference against aRNA from 1000 cell sample replicates.
The CGH array data was available from a previous study in which the bull was hybridized to two other animals using a dye swap design [ 29].
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We used a dye swap experimental design [ 99] and each sample was hybridized to two microarrays.
We used a dye swap experimental design [ 14, 15] and each sample was hybridized to two microarrays.
The experimental design used a dye swap procedure (see Methods) of uterine samples collected when a hard shelled egg was calcified in uterus (normal condition, N), or when the uterus was empty due to egg expulsion before onset of calcification (expelled condition, E).
Each pair (ET3-1 vs. experimental strain) was repeated using a dye-swap format to obviate dye bias.
RNA extracted from tissue samples was amplified and labeled using Ambion Message Amp I and hybridized on Agilent Human 1A glass arrays using a dye-swap replication scheme as described [11].
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