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Methods Mol Biol. 2018;1755:89-105. doi: 10.1007/978-1-4939-7724-6_7.

Making It All Work: Functional Genomics and Reporter Gene Assays.

Author information

1
Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
2
Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA.
3
Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
4
California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA, USA.
5
Johnsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
6
Department of Genomics, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org.
7
Functional Genomics Screening Team, The Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA. miraglia@gnf.org.

Abstract

Functional genomics is the study of the function of genes on a genome-wide level. Reporter gene assays can be utilized in this context to dissect signaling cascades, find new drug targets, or decipher the function of gene expression. The genome-wide scale of these experiments necessitates a different approach toward science than traditional single hypothesis driven research. High-throughput experimentation requires large project teams, automation, and discrete validation of each step in the automation and assay process. The purpose of this chapter is to provide a general outline of a standard functional genomics project with a reporter gene assay as readout, give an overview of the methodologies employed and familiarize the reader with the subsequent data analysis. The advantages of such high throughput experimentation are speed, quantitative results, and insights into biology on a genome-wide scale all of which enable a more rapid progress of science.

KEYWORDS:

Assay development; Automation; Data mining; Functional genomics; HTS; High-throughput screening; Liquid handling; Project management; RNAi; Reporter gene assays; Screening; cDNA; shRNA; siRNA

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