Array experiments microarrays

High-density DNA arrays or microarrays allow investigators to examine mRNA levels of all known genes in one experiment (see Lockhart and Winzeler 2000... 

Public repositories of microarray gene expression data have been developed to store the results of array experiments ArrayExpress (32) in Europe, Gene Expression Omnibus (GEO) in the United States (33), and the Center for Information Biology Gene Expression Database (CIBEX) (34) in Japan. Many journals already require an accession number (indicating that a data set has been submitted to one of these public databases) prior to publication. 

The dry lab portion of microarray analyses involves identifying the hybridized spots on the scanned tiff images (gridding) and defining the area and portion of the spot that should be quantified. Most often, mean or median pixel intensities for each spot are extracted from the tiff images. The result is a separate numeric value for each spot and each sample that represents the relative amount of sample hybridized to that spot. Thus, the raw results from an array experiment can be thousands... 

The use of a common reference RNA allows for the comparison of data between various array experiments. Typically a pool of RNA derived from a variety of tissues is used as a reference sample. Efforts are being made to implement common standards (MIAME, minimal information about a microarray experiment) for transcript profiling through the MGED Society to enable data sharing between different groups [50]. 

Microarray hybridization is a process by which nucleic acids are detected by hybridizing with complementary sequences bound to wafers at specific array coordinates. Hundreds to thousands of gene products may be measured in a single experiment. 

Spike-ins are usually RNA transcripts used to calibrate measurements in a DNA microarray experiment. Each spike-in is designed to hybridize with a specific control probe on the target array. Manufacturers of commercially available microarrays typically offer companion RNA spike-ins kits . Known amounts of RNA spike-ins are mixed with the experiment sample during preparation. Subsequently the measured degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA. 

It should be possible to extend the DNA microarray-binding experiment to whole-genome analysis of transcription factor binding sites. The authors suggest that a microarray spotted with 12,000 one-kilobase sequences would span the entire Saccharomyces cerevisiae genome (Bulyk et al., 2001). Such an array could be used to characterize the sequence specificity of S. cerevisiae transcription factors. These experiments would be useful for predicting functions of previously uncharacterized transcription... 

Pan W, Lin J, Le G. 2002. How many replicates of arrays are required to detect gene expression changes in microarray experiments A mixture model approach. Genome Biology 3(5) research0022.1. 

Ex situ (also known as spotted or printed) arrays have become very popular formats, especially for the building of custom noncommercial arrays used primarily by academic laboratories [see Association of Biomolecular Resource Facilities (ABRF) surveys on microarrays atwww.abrf.org]. The printed cDNA microarray was largely developed from gene expression work originating in the laboratories of RO. Brown and R.W. Davis at Stanford University (Schena et al., 1995). Plans for the construction of the microarrayer and split pin designs were available at the Brown lab website at http //cmgm.stanford.edu/ pbrown/mguide/index.html. This enabled researchers to prepare their own microarrays appropriate for their particular experiments. 

The manufacture and processing of the protein microarray should be conducted in such a manner that the arrayed proteins remain in their native and active state. For most proteins, this usually means the hydrated state in order to avoid surface denaturation. For antibody arrays which are perhaps more forgiving than other proteins, it has been our experience that while these could be stored cold and dry, it is most important to rehydrate them prior to use. This process is in sharp contrast to the preparation of nucleic acid arrays in which strand melting or denaturahon is necessary to achieve optimal binding to the solid support. While the hybridization process is well understood and can be controlled under thermodynamic principles, the folding and renaturation of proteins on planar (microarray) surfaces is under study. 

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