This research data supports “Nanopore microscope identifies RNA isoforms with structural colors” which is accepted in “Nature Chemistry”. The data set contains the source data for each figure (Figure 1 – Figure 5). LabVIEW code was used to collect and process data recorded using Axopatch 200B amplifier. Single events were isolated from the raw ionic current traces using a LabVIEW code and exported as Excel files.