MAGGY LTR-siRNA validation by 3' RACE. (A) Detailed schematic flow of small RNA (< 30 nt) isolation, polyadenylation, cDNA synthesis and specific MAGGY LTR-siRNA amplification. (B) PCR amplified MAGGY LTR-siRNAs using the 3' reverse primer and 5' MAGGY small RNA-specific primer under three different mycelia growth conditions separated on a 3% agarose gel (see Material and Methods for tissue growth treatments). L = 100 bp DNA Ladder (New England Biolabs), lanes 1 - 3 and 7 correspond to small RNA mapping to sense and lanes 4 - 6 to anti-sense strands. (C) PCR amplification of MAGGY LTR-siRNA 7 on a 15% polyacrylamide gel as described in (A) and (B) above (lanes 3, 6 and 9). For PCR controls, lanes 1, 4 and 7 were loaded with water and lanes 2, 5 and 8 with total RNA. D = Decade DNA ladder (Invitrogen).