ArticleMethods in molecular biology (Clifton, N.J.)2024
Using Publicly Available RNA-seq Data for Expression Analysis of Genes of Interest.
Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
RNA-seq data in publicly available repositories enable the efficient reanalysis of transcript abundances in existing experiments. Graphical user interfaces usually only allow the visual inspection of a single gene and of predefined experiments. Here, we describe how experiments are selected from the Sequence Read Archive or the European Nucleotide Archive, how data is efficiently mapped onto a reference transcriptome, and how global transcript abundances and patterns are inspected. We exemplarily apply this analysis pipeline to study the expression of photorespiration-related genes in photosynthetic organisms, such as cyanobacteria, and to identify conditions under which photorespiratory transcript abundances are enhanced.
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