Table 1.

Techniques for Measuring the Transcriptome, Proteome, Transcription, and Translation

	Technique	Pros
RNA abundance	Microarray	Inexpensive standardized
	RNA-seq	Measure unknown RNAs absolute quantitation
	SAGE	RNA-seq for 3′-UTR
	CAGE	RNA-seq for 5′-UTR
	Single-cell RNA-seq	Capture intercellular heterogeneity
RNA splicing	RNA-Pet TIF-seq	Identify splice-junctions and allele differences
	Long-read single-molecule Real-time sequencing	Capture splicing and allele data
	MapSplice SpliceMap	Identify splice junctions from RNA-seq data
	HMMsplicer
	MISO MATS	Quantify alternatively spliced genes
	SpliceR
Transcription	GRO-seq	Quantify nascent RNAs
	PAR-CLIP iCUP	Snapshot of transcribed RNAs (protein bound)
Translation	Ribo-seq	Snapshot of translated RNAs (ribosome bound)
Protein species and abundance	2D-PAGE	Provide visual display
	Shotgun, bottom-up LC/MS/MS	Easy to implement Measure many proteins
	MRM	Quantify known subset of proteins
	SWATH	Combine accurate quantitation with depth
	SILAC	Precise quantitation
	iTRAQ	Isobaric label Greater multiplexing
	Dimethyl-labeling	Least expensive, most amenable label
	Label-free quantitation	Amenable to many experimental workflows