Nanostring probes against lincRNA genes were designed following the standard nanostring design principles with the following modifications specifically for the lincRNA probes. (i) To exclude possible cross-hybridization, probes were screened for cross-hybridization against both the standard mouse transcriptome as well as a background database constructed from all the lincRNA sequences. (ii) To account for isoform coverage, a first pass design attempted to select a probe that would target as many isoforms as possible for each lincRNA. In cases where it was not possible to target all isoforms for a given lincRNA, the probe that targeted the largest number was selected, and additional probes were chosen when possible to target the remaining isoforms. (iii) The standard restrictions on Tm and sequence composition were relaxed to include probes for as many lincRNAs as possible.
