This conclusion is consistent with results from a whole-genome tiled microarray transcriptome study of E. coli MG1655 [ 34], which reported transcription of 4052 E. coli MG1655 genes in bacteria grown under different conditions, suggesting that about 98% of the E. coli MG1655 genes are transcribed.
Addressing these limitations, we undertook the current study of evaluating methods that combine stabilization of RNA and reduction of globin transcripts in whole blood to determine the suitability of the globin reduced RNA for microarray based transcriptome studies in sickle cell disease.
Previously, a number of microarray-based transcriptome studies of AD brains failed to identify the set of consistently deregulated genes across different studies [ 8].
Recall that the original master list was compiled using an earlier microarray circadian transcriptome study in just three tissues [ 42] and with the intention of finding genes with ubiquitously circadian transcripts.
Wang et al. [ 16] demonstrated that a data set of 10 million RNA-seq reads represented about 80% of annotated chicken genes, concluding that RNA-seq is a viable alternative to the microarray for transcriptome study.
Thereby, we generated a high-density oligonucleotide-based microarray platform for transcriptome studies in melon.
Since three-spine stickleback are an important ecological and evolutionary model-species as well as an emerging model for eco-toxicology, the ability to have a functional and flexible microarray platform for transcriptome studies will greatly enhance the research potential in these areas.
However, comprehensive experimental sRNA screening data is not yet available for the group of alpha-proteobacteria, with the exception of a tiling microarray-based transcriptome study in Caulobacter crescentus [ 29].
Results from RT-PCR in this study and microarray data from two transcriptome studies were further compared (see Additional files 2).
Although both RNAseq and microarray analyses measure the transcriptome, studies report different genes as DE using one method or the other, even when using the exact same samples [ 43– 43].
