Transcription profiling with microarrays has become a standard procedure for comparing the levels of gene expression between pairs of samples, or multiple samples following different experimental treatments. New technologies, collectively known as next-generation DNA sequencing methods, are also starting to be used for transcriptome analysis. These technologies, with their low background, large capacity for data collection, and dynamic range, provide a powerful and complementary tool to the assays that formerly relied on microarrays. In this chapter, we describe two protocols for working with microarray data from pairs of samples and samples treated with multiple conditions, and discuss alternative protocols for carrying out similar analyses with next-generation DNA sequencing data from two different instrument platforms (Illumina GA and Applied Biosystems SOLiD).
In the chapter we cover the following protocols:
- Basic Protocol 1: Comparing Gene Expression from Paired Sample Data Obtained from Microarray Experiments
- Alternate Protocol 1: Compare Gene Expression from Paired Samples Obtained from Transcriptome Profiling Assays by Next-Generation DNA Sequencing
- Basic Protocol 2: Comparing Gene Expression from Microarray Experiments with Multiple Conditions
- Alternate Protocol 2: Compare Gene Expression from Next-Generation DNA Sequencing Data Obtained from Multiple Conditions
To view the abstract, contents, figures, and literature cited online visit: Curr. Protoc. Bioinform. 27:7.14.1-7.14.34
To view the press release visit: Geospiza Team Publishes First Standard Protocol for Next Gen Data Analysis