The technical platforms to conduct ChIP-on-chip experiments are DNA microarrays, or “chips”. They may be categorized and distinguished in line with various traits:
- Probe type: DNA arrays can incorporate either automatically noticed cDNAs or PCR-merchandise, automatically noticed oligonucleotides, or oligonucleotides which might be synthesized in situ. The early variations of microarrays had been designed to stumble on RNAs from expressed genomic regions (open analyzing frames aka ORFs). Although such arrays are ideally suited to observe gene expression profiles, they have got constrained significance in ChIP experiments because maximum “exciting” proteins with respect to this technique bind in intergenic areas. Nowadays, even custom-made arrays may be designed and high-quality-tuned to fit the necessities of an experiment. Also, any sequence of nucleotides may be synthesized to cowl genic in addition to intergenic areas.
- Probe size: Early model of cDNA arrays had a probe period of about 200bp. Latest array versions use oligos as quick as 70- (Microarrays, Inc.) to 25 mers.
- Probe composition: There are tiled and non-tiled DNA arrays. Non-tiled arrays use probes selected consistent with non-spatial criteria, i.E., the DNA sequences used as probes have no fixed distances within the genome. Tiled arrays, but, choose a genomic vicinity (or maybe a whole genome) and divide it into equal chunks. Such a vicinity is referred to as tiled path. The average distance between every pair of neighboring chunks (measured from the center of each bite) gives the resolution of the tiled path. A path can be overlapping, quit-to-cease or spaced.
- Array size: The first microarrays used for ChIP-on-Chip contained about 13,000 noticed DNA segments representing all ORFs and intergenic areas from the yeast genome. Nowadays, Affymetrix gives complete-genome tiled yeast arrays with a resolution of 5bp (all in all 3.2 million probes). Tiled arrays for the human genome turn out to be increasingly effective, too. Just to name one example, Affymetrix offers a set of 7 arrays with approximately 90 million probes, spanning the complete non-repetitive part of the human genome with about 35bp spacing. Besides the real microarray, other tough- and software equipment is necessary to run ChIP-on-chip experiments. It is commonly the case that one company’s microarrays can not be analyzed with the aid of some other company’s processing hardware. Hence, buying an array requires additionally buying the related workflow device. The maximum important elements are, among others, hybridization ovens, chip scanners, and software programs for subsequent numerical analysis of the uncooked data.
