Microarray-based readout of chromatin immunoprecipitation (ChIP-chip) for high-throughput binding-site determination relies on specific antibodies which may not always be available.
The latest version of ArrayStar, version 5.0, which was released in 2011, also includes an optional module, QSeq, to allow scientists to visualize and analyze RNA-Seq and ChIP-Seq data using the same tools as are used for microarray gene expression.
From this set of candidate genes, microarray analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq and regulate the translation of RpoS (Sigma 38).
A long oligonucleotide can be designed for microarray analyses and dual-labeled oligonucleotides for probes such as molecular beacons.
However, with the invention of different types of microarray printing systems, hundreds of transfection mixes (containing different DNA of interest) may be printed on the same slide for cell uptake of plasmids.
More powerful queries are also possible including searching with lists of gene or protein names, drug names, metabolite names, GenBank IDs, Swiss-Prot IDs, Agilent or Affymetrix microarray IDs.