The Click-iT® RNA Alexa Fluor® 488 HCS Assay enables detection of global RNA transcription temporally and spatially in cells (PNAS (2008) 105:15779-84). The ability to detect newly synthesized RNA or changes in RNA levels resulting from disease, environmental damage or drug treatments is an important aspect of toxicological profiling. Utilizing an alkyne-modified nucleoside, 5-ethynyl uridine (EU), and powerful click chemistry, newly synthesized RNA can be detected without the use of radioactivity or antibodies with a simple, two-step procedure. In step one, the alkyne-containing nucleoside is fed to cells or animals and actively incorporated into nascent RNA. The small size of the tag enables efficient incorporation of the modified nucleoside into RNA, but not into DNA. Detection utilizes the chemoselective ligation or “click" reaction between and azide and an alkyne where the modified RNA is detected with a corresponding azide-containing dye. With its dimunitive “footprint", the Click-iT® detection molecule can easily penetrate complex samples and leaves open the possibility of multiplex analyses with other probes, including antibodies for the detection of RNA-interactive proteins for deeper biological insights.