Effect of MIR location and number within the 60-mer probes on signal intensity. Signals from hybridization of 60-mer probes with HeLa lcRNA are presented. (A) A set of three probes was considered for each MIR as follows: (1) MIR in the 5′; (2) MIR in the middle; (3) MIR in the 3′. For all three probes, the rest of the 60-mer sequence was composed of nonhuman genome sequences. Only probe sets for which the microarray signal of the MIR in the 5′ probe was >2000 were considered. For each probe set, the signal intensities for the three types of probes were calculated as a ratio of the signal intensity of the MIR in the 5′ probe. (B) Probes containing one, two (duplex), or three (triplex) copies of a MIR were analyzed. For each probe set, the signal intensities for the three types of probes were calculated as a ratio of the signal intensity of the probe containing one MIR copy. (C) Probes containing two or three MIR copies were analyzed. (None) Probes containing duplex or triplex MIRS, in which none of the MIR copies contain mismatches. (First) Duplex or triplex probes in which the 5′ MIR copy contains two mismatches. (Second) Duplex or triplex probes in which the 3′ or middle MIR copy, respectively, contains two mismatches. (Both) Duplex or triplex probes in which both the 5′ and the 3′ or middle MIR copies, respectively, contain two mismatches. For each probe set, the signal intensities for the three types of probes were calculated as a ratio of the signal intensity of the “None probe”. Data are presented as mean signal ratio ± SEM for 23 sets of probes, except for the triplex “First” set in C, for which two probes were eliminated from the calculation due to sequence matches to adaptors.
