Differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24 - Impact of the exclusion of polymorphic probes via a sequence-based approach

In order to identify differentially expressed genes in developing seeds of Arabidopsis thaliana three different stages of seed development were analysed (9-10, 10-11 and 12-13 days after flower opening) for two Arabidopsis thaliana accessions, Col-0 and C24. For each stage and accession three biological replicates were analysed. In order to compare transcriptomes of developing seeds of accessions Col-0 and C24 it was analysed which features of the ATH1-121501 array showed nucleotide exchanges and/or frame shifts when aligned to the genome sequence of C24. This information was used to generate a restricted data set exclusively consisting of probes that were identical to the genome sequences of both Col-0 and C24. Moreover, probes had to reveal perfect sequence alignments with TAIR10 representative gene models. Probe sets had to consist of three or more probes. Expression data for the two accessions were compared for developing seeds of the same stage. For each of the accessions gene expression at the different developmental stages was also compared. Please note that the biological material is identical to GSE94762 samples, but the data (both raw and normalized data) were corrected/processed in two different ways (as detailed in the sample data processing field)