Alice:Protocols
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Common Primers/Adaptors[edit]
Blunt-end adaptors: Solexa_1_up 5’ NH2- ACACTCTTTCCCTACACGACGCTCTTCCGATCT 3’OH Solexa_1_lo_nop 3’ NH2-ATGTGAGAAAGGGATGTGCTGCGAGAAGGCTAGA 5’OH TA adaptors (for the one adaptor protocol): PE_t_adapter 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT 3’OH t_adaptor_rc_s 3' CTTCTGCCGTATGCTCGAGAAGGCTAG 5’Phos regular Y adaptor: PE_t_adaptor(top) 5' ACACTCTTTCCCTACACGACGCTCTTCCGATC*T 3' PE_b_adaptor(bottom) 5' \\5phos\\GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG 3' For sequencing/library construction: Syb_FP5 5' ATGATACGGCGACCACCGAG 3' Syb_RP7 5' CAAGCAGAAGACGGCATACGAG 3' For Nextera protocol: Adaptor 1 5'-AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAG-3' Adaptor 2 (IDX2) 5'-CAAGCAGAAGACGGCATACGAGATACATCGCGGTCTGCCTTGCCAGCCCGCTCAG-3' Adaptor 2 (IDX4) 5'-CAAGCAGAAGACGGCATACGAGATTGGTCACGGTCTGCCTTGCCAGCCCGCTCAG-3' Adaptor 2 (IDX5) 5'-CAAGCAGAAGACGGCATACGAGATCACTGTCGGTCTGCCTTGCCAGCCCGCTCAG-3' Adaptor 2 (IDX6) 5'-CAAGCAGAAGACGGCATACGAGATATTGGCCGGTCTGCCTTGCCAGCCCGCTCAG-3' Adaptor 2 (IDX7) 5'-CAAGCAGAAGACGGCATACGAGATGATCTGCGGTCTGCCTTGCCAGCCCGCTCAG-3' Nextera Primer 1: 5'-AATGATACGGCGACCACCGA-3' Nextera Primer 2: 5'-CAAGCAGAAGACGGCATACGA-3' Nextera Primer 2 Index 2: 5' CAAGCAGAAGACGGCATACGAGATACATCG 3' Nextera Primer 2 Index 4: 5' CAAGCAGAAGACGGCATACGAGATTGGTCA 3' Nextera primer 2 Index 5: 5' CAAGCAGAAGACGGCATACGAGATCACTGT 3' Nextera primer 2 Index 6: 5' CAAGCAGAAGACGGCATACGAGATATTGGC 3' Nextera primer 2 Index 7: 5' CAAGCAGAAGACGGCATACGAGATGATCTG 3'