soil eukaryotic 18S SSU rRNA diversity in three neotropical broadleaf forests
Two-step amplification with 1) ciliate specific primers, and 2) universal V4 primers.  The ciliate specific primers are Cil_F 5' - TGG TAG TGT ATT GGA CWA CCA -3' and Cil R (an equimolar mix of three different primers): 5' - TCT GAT CGT CTT TGA TCC CTT A  3', 5' - TCT RAT CGT CTT TGA TCC CCT A  3' and 5' - TCT GAT TGT CTT TGA TCC CCT A  3'.  Cycling conditions (with Hot Start Taq from Qiagen) are 1) 95C 5 min, 2) 94C 30 sec, 3) 56C 30 sec ,4) 72C 60 sec, repeat 2-4 = 25x, 5) 72C 10 min.  Followed by an amplification with universal 18S SSU rRNA V4 primers (see other sequencing runs in the same bioproject).