The microarray probes detect transcripts of this phosphatidylserine decarboxylase pseudogene that arise from loci on five different chromosomes (5, 11, 14, 17 and Y).
We were making the assumption that the microarray probes detect the orthologous ovine transcript and previous results indicate that this was the case [47], [48].
In this study, we have optimized the RNA preparatory steps and used an amplification and labeling system specifically developed for analysis of degraded RNA, along with a microarray containing probes detecting sites across the whole transcript.
The DNA microarray covers 333 oligonucleotide probes, detecting resistance and virulence genes.
The number of probe sets for the different GO terms was computed for groups of probe sets defined according to different criteria (such as whole microarray probe sets, detected probe sets or probe sets belonging to a given cluster).
Although microarray probes failed to detect increased Wnt7a expression, our independent study confirms up-regulation of Wnt7a in Pkd1 -/- animals (Qin et al, submitted).
The cross hybridization potential of the microarray was representative of 10,362 probes detected in both channels, while 12,052 probes hybridised to S. japonicum and 11,254 probes hybridised to S. mansoni.
Here we considered that a gene was expressed if any of the probes detecting that gene in the microarray was called as 'expressed' according to the Barcode method.
Raw microarray data were preprocessed and normalized using the robust multichip average algorithm (RMA) [ 22, 23], keeping only probes detected in at least 60% of the samples.
The slight differences between the results, therefore, may have resulted from the characteristics of each method, because PCR primers target short sequences with high similarity, while microarray probes overall similarity to detect the target sequence.
In the meristematic zone, AtPHT1 8 and AtPHT1 9 transcripts are generally as abundant, if not more abundant, than the transcripts recognised by the redundant microarray probe sets that detect the sum of AtPHT1 1 + AtPHT1 2 transcripts or the sum of AtPHT1 4 + AtPHT1 7 transcripts (Additional file 10: Table S1).
