Table 1.

Summary of the most common methods for mRNA quantification and transcription analysis

	Northern	MIcroarray	Real time PCR	RNA seq	CHiP-CHiP	FISH	MS2
	ensemble	ensemble	ensemble	ensemble	ensemble	Single cell	Single cell
Determining mRNA expression
measuring	Total mRNA	Total mRNA	Total mRNA	Total mRNA		Total mRNA	Total mRNA
Detection method	Blotting to membrane/ hybridization with synthetic probe	RNA labeling/ Hybridization to array	Reverse transcription/ PCR	mRNA fragmentation/ adaptor ligation/ amplification/ sequencing		Probe hybridization in situ	Insertion of repeats/ Binding of fluorescent protein
mRNA quantification	relative intensity	relative intensity	Absolute numbers requires standard	Single molecule counting		Single molecule counting	Single molecule counting
Number of genes	1 per cell	Genome wide	many	Genome wide		1–3 per cell	1 per cell
Measuring transcription
measuring					Polymerase association	nascent mRNAs	nascent mRNAs
Detection method					Fragmentation/IP/ Amplification/ hybridization to array	Hybridization using fluorescent probes	Insertion of repeats/ Binding of fluorescent protein
quantification					relative changes in polymerase loading	Counting of nascent mRNAs	Relative intensity of mRNA signal
Number of genes					Genome wide	1–3 per cell	1 per cell