Abstract: The present invention relates to rRNA-derived cDNA used as an internal standard or control to achieve normalization of hybridization signal detection in microarray biochip technology. Analysis of data obtained from a laser scanner during DNA microarray experiments first requires image processing. However, the data generated for the arrayed genes must be normalized before differentially expressed genes can be identified. Normalization is necessary to compensate for differences in labelling and detection efficiencies for the labels and for differences in the quantity of starting RNA from the samples examined in the assay. Because of its relatively invariant expression across tissues and treatments, 18S and 28S ribosomal RNAs are ideal internal controls for quantitative RNA analysis. A way to circumvent the technical difficulties of using ribosomal RNA as a control, because of its overabundance relative to that of other RNAs, is described and claimed in the present application.

Abstract: The methods and products that are described in the present patent application are designed to determine by serial analysis the transcriptional activation pathways used by any compound of interest that is biologically active in a cell. We have engineered a library of transgenic or recombinant cell lines that allow the identification of simultaneous transcriptional pathways possibly used by the compound. Each cell line constituting the library has been engineered by stable transfection thereof by retroviral integration, to carry a reporter gene under the transcriptional control of a particular transcription factor or family thereof endogenous to the host cell. This is achieved by having the expression of the reporter gene driven by a minimal promoter and a transcription factor responsive-element (TF-RE) or a tandem or concatemer thereof.

Abstract: The invention provides a novel method for the screening and for the identification of nucleic acid binding factors (NABFs) or nucleic acid binding elements (NABEs) that are differentially active between two phenotypically different cell lines (normal and modified); in a particular cell type before and after a given treatment; or between two completely heterologous cell lines. The invention also provides methods for the simultaneous analysis of the effect of given compounds on multiple DNA-protein interactions. It further provides for the analysis of compounds that are nucleic acid binding factor analogs and compounds that selectively bind cis-acting nucleic acids.