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Log-transformed dot intensity for the abundant transcript probes versus control probe [see Additional file 2] were plotted and PCR products corresponding to spots with low intensity measures for the control probe excluded from further analysis.
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If we have abundant transcript sequences for crab-eating macaque, we could design the whole gene probe sequences for microarray analyses.
The most abundant transcript in FDE list was SDR65C, reflecting its importance in laticifer differentiation.
Interestingly, we also found an abundant transcript encoding RNase 1.
A lower delta Ct value indicates more abundant transcript.
The most highly abundant transcript was ribulose bisphosphate carboxylase (RuBisCO).
As described above, boPAG-2 was an extremely abundant transcript.
The gap2 transcript was abundant across all experiments, in particular in phototrophic conditions, where it reached 47% of the most abundant transcript in vegetative cells.
We designed ~100 oligonucleotide probes matching these abundant transcripts [see Additional file 1] to use in a library subtraction procedure to minimize EST redundancy.
Probe sets that were saturated by very abundant transcripts also were excluded from the analysis.
Importantly, we have demonstrated here that the number of probe sets detected shows a high level of retention with lowering RNA input levels in two different probe generation methods, impacting only the most abundant transcripts at low input levels in the One-Direct system.
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