An RNA-Seq protocol for differential expression analysis
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Nick DL Owens Elena De Domenico Michael J GilchristAbstract
Here we consider RNA-Seq, used to measure global gene expression through RNA fragmentation, capture, sequencing, and subsequent computational analysis. Xenopus, with its large number of RNA-rich, synchronously developing, and accessible embryos, is an excellent model organism for exploiting the power of high-throughput sequencing to understand gene expression during development. Here we present a standard RNA-Seq protocol for performing two-state differential gene expression analysis (between groups of replicates of control and treated embryos) using Illumina sequencing. Samples contain multiple whole embryos, and polyadenylated mRNA is measured under relative normalization. The protocol is divided into two parts: wet-lab processes to prepare samples for sequencing and downstream computational analysis including quality control, quantification of gene expression, and differential expression.
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Journal Cold Spring Harbor Protocols
Volume 2019
Issue number 6
Pages pdb.prot098368
Available online
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Publisher website (DOI) 10.1101/pdb.prot098368
Europe PubMed Central 30952685
Pubmed 30952685
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