Table 3.

Comparison of characteristics for 4tU-labeling, TRAP and INTACT methods.

	4tU-labeling, pulse (< 1 hour)	4tU-labeling (several hours)	TRAP	INTACT
mRNA	+	+	+	+
rRNA	+	+	+	+
tRNA	+	+	-	+
non-coding RNA	+	+	+ (subset)	+
unprocessed RNA	+	+	-	+
highly dynamic RNA populations	++	+	+	+
“steady-state” RNA pool	-	+	+	+/-
cell-type specific RNA population	+	+	+	+
identifies differences in RNA expression before and after treatment or in disease models	++	+	+	+
possible biases	rRNA is highly abundant and could bias RNAseq libraries, especially if the number of mRNA transcripts is limited	rRNA abundance	some long intergenic noncoding RNAs display low ribosome binding; differences in ribosomal occupancy of transcripts	rRNA abundance,  transcripts encoding proteins regulating transcription and mitosis might be overrepresented
purification steps described before RNAseq	rRNA depletion	rRNA depletion	-	none described