Alice:Protocols

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  1. probe preparation
  2. cosmic probe elongation
  3. Shotgun Sequencing Library prep-MmeI

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'