Table 1.

RNA-Seq library protocols

Library design Usage Description
Poly-A selection Sequencing mRNA Select for RNA species with poly-A tail and enriches for mRNA
Ribo-depletion Sequencing mRNA, pre-mRNA, ncRNA Removes ribosomal RNA and enriches for mRNA, pre-mRNA, and ncRNA
Size selection Sequencing miRNA Selects RNA species using size fractionation by gel electrophoresis
Duplex-specific nuclease Reduce highly abundant transcripts Cleaves highly abundant transcripts, including rRNA and other highly expressed genes
Strand-specific De novo transcriptome assembly Preserves strand information of the transcript
Multiplexed Sequencing multiple samples together Genetic barcoding method that enables sequencing multiple samples together
Short-read Higher coverage Produces 50–100 bp reads; generally higher read coverage and reduced error rate compared to long-read sequencing
Long-read De novo transcriptome assembly Produces >1000 bp reads; advantageous for resolving splice junctions and repetitive regions

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  1. Published in Advance April 13, 2015, doi: 10.1101/pdb.top084970 Cold Spring Harb Protoc 2015: pdb.top084970-
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