By way of example, OJ Rando and collaborators [ 11] analyzed 12 histone modifications at nucleosomal resolution by hybridizing a high-density tiling microarray with mononucleosome fragments obtained after micrococcal nuclease treatment.
The ability of AT- and TC-specific probes to correctly predict the expression divergence from the mid-parent value was verified experimentally by hybridizing Affymetrix microarray chips with the 1 1 mix of AT and TC RNA samples and fitting the model assuming the 1 1 ratio of AT and TC expression in the mix.
By hybridizing the microarray with total RNA from different mouse embryonic stages and from mouse embryonic stem (ES) cells, and comparing this data with existing next generation sequence (NGS) data, we were able to show that the majority of UCEs which have been shown to act as enhancers during mouse development are also transcribed and investigated salient properties of these transcripts.
Total RNA extracted from environmental samples was used to determine the composition of the metabolically active members of the microbial community and then to compare the biofilm and planktonic environmental transcriptomes by hybridizing to a genomic microarray of L. ferrooxidans.
This method, known as "ChIP-on-chip", is based on chromatin immunoprecipitation (ChIP) assay, and identifies the enriched DNA fragments by hybridizing to microarrays with probes corresponding to genomic regions of interest [26] [28].
Over the last several years, great strides have been made in expanding the use of ChIP from a one gene-at-a-time approach to a global type of analysis by hybridizing samples to genomic microarrays (i.e., ChIP-on-chip assay) [ 26].
The hybridization solution was hybridized to a microarray slide using a home built hybridization station for 2 h at 37°C with agitation by bubble movements.
One approach to microarray-based genomic research is to use cross-species hybridization (CSH) by hybridizing RNA of the studied organism to a microarray chip which contains transcripts of genes of a closely related species.
A patient would be tested by hybridizing mRNA from the tumor to a microarray, applying gcrma to this microarray and the reference set together, and determining the sample's AP4 status using cutoffs determined with the reference samples.
In the present study, we tested the feasibility of identifying genetic polymorphism in melon crops by hybridizing gDNA to custom-designed microarrays based on a partial transcriptome.
