Disclosed herein is a method of selectively labeling non-
messenger RNA molecules by isolating
total RNA from a tissue or
cell, dissolving the isolated
RNA, optionally blocking 3′ ends of the
RNA, and adding T4
RNA ligase and a labeled
nucleic acid adaptor, with the result that the T4 RNA ligase ligates the adaptor to RNA having a 5′
phosphate group such as small RNAs. A method of labeling the 5′ end of mRNA isolates
total RNA from a tissue or
cell; dissolves RNA in RNase-
free water; removes a 5′ cap structure from the mRNA using tobacco acid
pyrophosphatase (TAP); removes the TAP; optionally blocks the 3′ end of the RNA molecules using TdT with ddA, ddT, ddG, ddC or a combination thereof; and ligates an adaptor to the RNA by adding T4 RNA ligase and a labeled
DNA or RNA adaptor. A method of amplifying and labeling noncapped RNAs and / or capped RNAs is useful in
expression analysis of the whole-
genome transcripts from cells and tissues. Sense and antisense transcripts are labeled from different experimental approaches. In another embodiment, there is disclosed a method of
sequence selection and probe design. Probes are designed complementary to the labeled target RNA. For small RNAs, sequences are selected for detections of mature, counterparts (ig miR*), and precursors. In another embodiment, there is disclosed a method of expression profiling
small RNA by providing labeled
small RNA, providing a
microarray comprising a plurality of probes hybridizable to
small RNA, incubating the labeled small RNA with the
microarray, washing unhybridized RNA from the
microarray and
drying the microarray,
staining hybridized RNA on the microarray; and scanning the labeled microarray to determine the identity and quantity of labeling to the various mRNA probe sites and thus providing an expression profile of small RNA.