Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression...

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• High-throughput cDNA sequencing of poly(A)-enriched RNA is an emerging technology.
• It aims to replace microarrays for quantitative gene expression measurement.

Purpose of the Study:

• Compare full-length cDNA sequencing to 2-channel gene expression microarrays.
• Evaluate their effectiveness in measuring differential gene expression.

Main Methods:

• Focused on data from a single Illumina 1G sequencer lane due to comparable cost to microarrays.
• Compared sequencing data against a highly replicated microarray experiment.
• Utilized a large number of quantitative PCR (qPCR) assays for validation.

Main Results:

• Neither cDNA sequencing nor microarrays were decisively superior for differential gene expression measurement.
• Full-length cDNA sequencing identified heterozygosity in a diploid hybrid of S. cerevisiae.
• Quantitative allele-specific expression was measured simultaneously with sequencing.

Conclusions:

• Full-length cDNA sequencing offers a viable alternative to microarrays for gene expression studies.
• This technology provides additional insights into genetic variation and allele-specific expression.
• Further research can leverage cDNA sequencing for comprehensive genomic analysis.