Microarrays and chips

The composition of the genome determines many biological processes in an organism, thereby influencing the susceptibility toward genetic diseases or the response to xenobiotic compounds." The transcriptome is the complete set of RNA products that can be produced from the genome, and transcriptomics is the study of the transcriptome. For example, microarrays and chips represent... 

Different variations of ChIP experiments are now rapidly evolving. This is mainly due to the rapid progress in the field of microarrays and next-generation sequencing that can be used for the analysis of the immunopreciptated DNA. We discuss here the most important variations of the standard ChIP protocol with a focus on ChIP-on-chip and ChIP-sequencing technologies. 

The data for this example was derived from the supplementary material of the estrogen receptor (ER) ChIP-on-chip publication of Carroll et al. [20]. The dataset consists of three replicates of specific enrichments for the estrogen receptor alpha and RNA Polymerase II versus input controls. All three replicates were performed on the Affymetrix human tiling 1.0 microarrays (14-chip set). 

Figure 6.26. Gene Expression Analysis Using Microarrays. The expression levels of thousands of genes can he simultaneously analyzed using DNA microarrays (gene chips). Here, analysis of 1733 genes in 84 hreast tumor samples reveals that the tumors can he divided into distinct classes based on their gene expression patterns. Red corresponds to gene induction and green corresponds to gene repression. [Adapted from C. M. Perou et al, Nature 406(2000) 747.]...

Potential new technological developments that may results from these discoveries include nanobiological devices, micromachines, nanoelectronic devices and protein microarrays and next-generation computer chips (Alkire and Braatz, 2005 [179] Sematech, 2005 [187]). These examples represent only a few of many potential technologies on the horizon that we cannot hope to understand, develop, or utilize in a timely manner without simulation-based engineering methods. 

Wheeler DB, Carpenter AE, Sabatini DM (2005) Cell microarrays and RNA interference chip away at gene function. Nat Genet 37 S25-S30... 

There are two formats of microarray oligonucleotide chips contain short (less than 60) nucleotides synthesized in situ on the solid support (1,2) and spotted DNA arrays where nucleic acids are robotically spotted onto a glass substrate (3). PCR product or plasmid DNA in 96/384-well format is transferred by specially engineered tips to multiple glass slides then dried and fixed to the glass substrate. 

Recent research efforts using microarray DNA chips (Biochemical Methods 18.1) have provided some of the details of the molecular mechanisms by which HIV disrupts the functioning of T-4 lymphocytes. By monitoring the mRNA expression of over 6000 genes simultaneously, researchers tracked the consequences of HIV infection. They observed that within 30 minutes of infection, the expression of about 500 cellular genes had been suppressed and 200 had been activated. Within hours, host cell mRNA had largely been... 

Genes specific for a particular tissue can be expressed differently under a variety of different metabolic conditions or stresses within the cell or organism. Tracking mRNA and protein expression as different indicators of gene activity in normal and disease tissue is now one of the more important methods for gene validation. This type of analysis involves extensive use of DNA microarrays and related chip technologies (31-33). 

---