High throughput assay for identification of gene expression modifiers

A method of screening a plurality of test compounds to identify one or more compounds that affect expression of at least one trapped gene comprising the steps of:

• a) providing a gene-trap vector encoding a fluorescent reporter protein, wherein the fluorescent reporter protein directly or indirectly produces fluorescence;
• b) stably transfecting a population of cells with the gene-trap vector, wherein expression of the reporter protein is indicative of the expression of the trapped gene;
• c) sorting the population of stably transfected cells by FACS into groups according to expressed levels of reporter protein;
• d) distributing cells from each group into one or more pools, wherein each pool represents more than one trapped gene;
• e) expanding the cells from each pool, wherein the expansion is such that a sufficient number of cells representing each trapped gene are produced to permit distinction of the effect of a test compound on the expression of the trapped gene over a control;
• f) placing the expanded cells into individual wells;
• g) incubating the wells from each pool in the absence or presence of a plurality of test compounds to generate control wells and test wells respectively, wherein the plurality of test compounds are added to the same wells well or separate wells;
• h) conducting FACS analysis on the test wells and control wells to generate fluorescence distribution patterns for the cells in the test wells and control wells;
• i) comparing the fluorescence distribution patterns of each test well with the control well;
• and
• j) identifying the test well in which the fluorescence distribution pattern differs from the control well, wherein identification of a different fluorescence distribution pattern is indicative of a test compound affecting the expression of one or more trapped gene represented in the test well,
• wherein the sorting parameters are adjusted to compensate for heterogeneity in the reporter protein fluorescence due to cell cycling and wherein the cell stream velocity during FACS analysis is less than 25 meters per second, and wherein background fluorescence is reduced by illuminating white light on the sample.

A method of identifying multiple modulators of a known trapped gene comprising the steps of

• a) obtaining a clone of stably transfected cells in which the known gene has been trapped by a gene-trap vector encoding a fluorescent reporter protein has been inserted, wherein the fluorescent reporter protein directly or indirectly produces fluorescence;
• b) placing cells from the clone into multiple wells;
• c) incubating the wells in the absence or presence of a plurality of test compounds to generate control wells and test wells respectively, wherein the plurality of test compounds are added to the same wells well or separate wells;
• d) conducting FACS analysis on the test wells and control wells to generate fluorescence distribution patterns for the cells in the test wells and control wells;
• e) comparing the fluorescence distribution patterns of each test well with the control well;
• and
• f) identifying the test wells in which the fluorescence distribution pattern differs from the control well, wherein identification of a different fluorescence distribution pattern is indicative of a test compound affecting the expression of the trapped gene,
• wherein the sorting parameters are adjusted to compensate for heterogeneity in the reporter protein fluorescence due to cell cycling, wherein the cell stream velocity during FACS analysis is less than 25 meters per second, and wherein background fluorescence is reduced by illuminating white light on the sample.