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Levels of mRNA can be quantitatively measured by  northern blotting
 , which provides size and
sequence information about the mRNA molecules. A sample of RNA is separated on
an  agarose gel  and hybridized to a
radioactively labeled RNA probe that is complementary to the target sequence.
The radiolabeled RNA is then detected by an  autoradiograph
 . Because the use of radioactive
reagents makes the procedure time-consuming and potentially dangerous,
alternative labeling and detection methods, such as digoxigenin and biotin
chemistries, have been developed. Perceived disadvantages of Northern blotting
are that large quantities of RNA are required and that quantification may not
be completely accurate, as it involves measuring band strength in an image of
a gel. On the other hand, the additional mRNA size information from the
Northern blot allows the discrimination of alternately spliced transcripts.

Another approach for measuring mRNA abundance is RT-qPCR. In this technique, 
reverse transcription 
is followed by  quantitative PCR 
. Reverse transcription first generates a DNA template from the mRNA; this
single-stranded template is called  cDNA  . The cDNA template is then amplified in the quantitative
step, during which the  fluorescence 
emitted by labeled  hybridization probes  or  intercalating dyes
 "Intercalation \(biochemistry\)")
changes as the  DNA amplification  process progresses. With a carefully constructed
standard curve, qPCR can produce an absolute measurement of the number of
copies of original mRNA, typically in units of copies per nanolitre of
homogenized tissue or copies per cell. qPCR is very sensitive (detection of a
single mRNA molecule is theoretically possible), but can be expensive
depending on the type of reporter used; fluorescently labeled oligonucleotide
probes are more expensive than non-specific intercalating fluorescent dyes.

For  expression profiling  , or high-throughput analysis of many genes within a sample, 
quantitative PCR  may be performed
for hundreds of genes simultaneously in the case of low-density arrays. A
second approach is the  hybridization microarray  . A single array or "chip" may contain probes to determine
transcript levels for every known gene in the genome of one or more organisms.
Alternatively, "tag based" technologies like  Serial analysis of gene
expression  (SAGE) and  RNA-Seq  , which can
provide a relative measure of the cellular  concentration
 of different mRNAs, can be used. An
advantage of tag-based methods is the "open architecture", allowing for the
exact measurement of any transcript, with a known or unknown sequence. Next-
generation sequencing (NGS) such as  RNA-Seq  is
another approach, producing vast quantities of sequence data that can be
matched to a reference genome. Although NGS is comparatively time-consuming,
expensive, and resource-intensive, it can identify  single-nucleotide
polymorphisms  , splice-variants, and novel genes, and can also be used to
profile expression in organisms for which little or no sequence information is
available.