A whole-genome microarray comprising probes covering all the ORFs present on the chromosome and the six plasmids (Alpha, Beta, Gamma, Delta, Epsilon and Zeta) of Nostoc, was designed as described previously [ 15].
The custom made microarray contained 97 probes, covering whole S. pneumoniae tmRNA sequence (see Additional file 1).
In this study, we have designed custom microarray chips with probes covering majority of annotated genes from the MSU database.
The comparative genomic hybridization (CGH) microarray featured overlapping probes covering the entire C. botulinum A1 strain ATCC 3502 genome sequence [GenBank: AM412317].
To characterize the contribution of transposons to mammalian transcriptomes, we developed a custom microarray platform with probes covering known human and mouse transposons in both sense and antisense orientations.
We employed custom DNA microarrays that contained probes covering 10 kb of genomic sequences flanking the transcription start site (TSS) of 5000 genes selected from our pervious microarray studies and related literatures.
Therefore, we repeated the analysis shown in Fig. 2, but hybridised the chromatin immunoprecipitates to microarrays containing oligonucleotide probes covering all of the budding yeast genome.
Validation of miRNA microarray was performed on Illumina Human v2 microarray, containing 1146 miRNA probes (covering 95% of miRBase1 v12.0 known human miRNAs).
The probes were hybridized to two Illumina MouseRef-8 v2.0 BeadChips that carry 8 microarrays each, containing 25,697 probes covering 19,728 non-redundant, well-annotated RefSeq sequences covered by either one single probe (79.3%), 2 probes (15%) or 3 or more probes (5.7%).
A 4 × 44 K 60-mer oligo microarray consisting of 43,833 probes covering 42,440 unigene sequences and 1417 positive and negative Agilent control sequences was designed and used to analyze the expression profiles of four tea plant clones.
