Table 2.

Selected high-throughput methods for identifying lncRNAs

Method	Purpose	Reference
Tiling microarray	Transcripts and transcriptome analysis	[15, 16]; plant references [17–20]; plant lncRNAs references [20–25]
Serial analysis of gene expression (SAGE)	Transcripts and transcriptome analysis	[26]; plant references [27–30]
Massively parallel signature sequencing (MPSS)	Transcripts and transcriptome analysis	[31]; plant references [32–35])
Cap analysis of gene expression (CAGE, CAGE-seq)	Identify transcripts with 5´ caps	[36, 37]; plant references [38–40]; protocol [41, 42]
RNA-seq	Transcripts and transcriptome analysis	First report [43] and comprehensive review by Wang et al. [4]; in this book: RNA-seq protocols (Part IV, Chapters 11–16), biotic and abiotic stress-related protocol (Part III, Chapters 8–10)
Parallel analysis of RNA ends (PARE)/genome-wide mapping of uncapped and cleaved transcripts (GMUCT)/degradome-seq	Identify transcripts that are being degraded and/or microRNA targets	PARE: [44], protocol [45]; GMUCT: [46], protocol [47]; degradome sequencing [48], protocol [49]
Transcript isoform sequencing (TIF-seq)	High-throughput identification of transcript isoforms with 5´ caps and poly(A) tails	[50]; protocol [51]
Global run-on sequencing (GRO-seq)	Identify the binding sites of transcriptionally active RNA Pol II and nascent RNAs	[52]; plant references [53, 54]; protocol [55, 56]
Precision nuclear run-on sequencing (PRO-seq)	Identify the binding sites of transcriptionally active RNA Pol II and nascent RNAs	[57]; protocol [58]
Native elongating transcript sequencing (NET-seq)	Identify the binding sites of elongating RNA Pol II and the associated nascent RNAs	[59–61]; protocols [62–64]
BRIC-Seq/BrU-Seq/BrUChase-Seq	Identify nascent RNAs and RNA half-lives, and measure RNA decay	BRIC-seq:[65], protocol [66, 67]; BrU-seq/BrUChase-seq: [68], protocol [69]