Illumina GA/Oligo info: Difference between revisions

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>Alan6017518
>Alan6017518
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==Nextera Read Primer==
==Nextera Read Primer==
Nextera Read 1 Primer: 5'-GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG-3'  
{| {{table}}
Nextera Read 2 Primer: 5'-GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG-3'
| align="center" style="background:#f0f0f0;"|'''Sequence ID'''
Nextera Index Read Primer: 5'-CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCG-3'
| align="center" style="background:#f0f0f0;"|'''Sequence'''
|-
| Nextera Read 1 Primer||5'-GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG-3'  
|-
| Nextera Read 2 Primer|| 5'-GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG-3'
|-
| Nextera Index Read Primer|| 5'-CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCG-3'  
|
|}

Revision as of 04:33, 9 January 2011

Name in original paper Nick-name Sequence (5\'->3\') Sequence Modification Reference
A_adapter_t Long Y-adaptor (top) AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T 3'-Phosphorothioate bond [1]
A_adapter_b Long Y-adaptor (bottom) GATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG None [1]
PE_t_adapter Regular Y-adaptor (top) ACACTCTTTCCCTACACGACGCTCTTCCGATC*T 3'-Phosphorothioate bond [2]
PE_b_adapter Regular Y-adaptor (bottom) /5Phos/GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG 5'-phosphorylation [2]
PCR_F Sol. Amp. (Forward) AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T 3'-Phosphorothioate bond [2]
PCR_R Sol. Amp. (Reverse) CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC*T 3'-Phosphorothioate bond [2]
Syb_FP5 Sol. Quant. (Forward) ATGATACGGCGACCACCGAG None [2]
Syb_RP7 Sol. Quant. (Reverse) CAAGCAGAAGACGGCATACGAG None [2]
PE_t_N2 Y-adaptor for MmeI ligation (top) ACACTCTTTCCCTACACGACGCTCTTCCGATCTN*N 3'-Phosphorothioate bond
PE_N2 Y-adaptor for MmeI ligation (top) ACACTCTTTCCCTACACGACGCTCTTCCGATC*NN 3'-Phosphorothioate bond
PE_b_A Y-adaptor for MmeI ligation (bottom) /5Phos/AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG 5'-phosphorylation
PE_t_Met bis-seq(Forward) A/iMe-dC/A/iMe-dC/T/iMe-dC/TTT/iMe-dC//iMe-dC//iMe-dC/TA/iMe-dC/ACGACG/iMe-dC/T/iMe-dC/TT/iMe-dC/CGAT/iMe-dC/*T 3-phosphorothiate, 5'-Methyl
PE_b_Met bis-seq (Reverse) /5Phos/GATCGGAAGAGCGGTT/iMe-dC/AG/iMe-dC/AGGAATG/iMe-dC/CGAG 5'-phosphorylated, 5'-Methyl
RC_PE_t_adapter RC_Regular Y-adaptor with Biotin (top) /5Biosg/TTTTTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT 5'-Biotin
RC_PE_b_adapter RC_Regular Y-adaptor with Biotin (bottom) /5Biosg/TTTTTTTCTCGGCATTCCTGCTGAACCGCTCTTCCGATC 5'-Biotin
Small RNA Sequencing Primer Solexa-TSS-Seq CGACAGGTTCAGAGTTCTACAGTCCGACGATC

Library Free Multiplexing Primers

Name Nick-name Sequence (5\'->3\') Sequence Modification Reference
Left Probe Linker, No barcode (forward) AmpF6.3Sol AATGATACGGCGACCACCGACACTCTCAGATGTTATCGAGGTCCGAC None None
Right Probe Linker, Barcode 1: CGTGAT (reverse) AmpR6.3Ind1 CAAGCAGAAGACGGCATACGAGATCGTGATGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 2: ACATCG (reverse) AmpR6.3Ind2 CAAGCAGAAGACGGCATACGAGATACATCGGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 3: GCCTAA (reverse) AmpR6.3Ind3 CAAGCAGAAGACGGCATACGAGATGCCTAAGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 4: TGGTCA (reverse) AmpR6.3Ind4 CAAGCAGAAGACGGCATACGAGATTGGTCAGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 5: CACTGT (reverse) AmpR6.3Ind5 CAAGCAGAAGACGGCATACGAGATCACTGTGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 6: ATTGGC (reverse) AmpR6.3Ind6 CAAGCAGAAGACGGCATACGAGATATTGGCGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 7: GATCTG (reverse) AmpR6.3Ind7 CAAGCAGAAGACGGCATACGAGATGATCTGGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 8: TCAAGT (reverse) AmpR6.3Ind8 CAAGCAGAAGACGGCATACGAGATTCAAGTGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 9: CTGATC (reverse) AmpR6.3Ind9 CAAGCAGAAGACGGCATACGAGATCTGATCGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 10: AAGCTA (reverse) AmpR6.3Ind10 CAAGCAGAAGACGGCATACGAGATAAGCTAGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 11: GTAGCC (reverse) AmpR6.3Ind11 CAAGCAGAAGACGGCATACGAGATGTAGCCGCTAGGAACGATGAGCCTCCAAC None None
Right Probe Linker, Barcode 12: TACAAG (reverse) AmpR6.3Ind12 CAAGCAGAAGACGGCATACGAGATTACAAGGCTAGGAACGATGAGCCTCCAAC None None
Sequencing reading primer AmpR6.3IndSeq GTTGGAGGCTCATCGTTCCTAGC None None

Multiplex primers for the N2-adaptor

Sequence ID Sequence
PCR_R.N2Ind1 CAAGCAGAAGACGGCATACGAGATCGTGATCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind2 CAAGCAGAAGACGGCATACGAGATACATCGCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind3 CAAGCAGAAGACGGCATACGAGATGCCTAACTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind4 CAAGCAGAAGACGGCATACGAGATTGGTCACTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind5 CAAGCAGAAGACGGCATACGAGATCACTGTCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind6 CAAGCAGAAGACGGCATACGAGATATTGGCCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind7 CAAGCAGAAGACGGCATACGAGATGATCTGCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind8 CAAGCAGAAGACGGCATACGAGATTCAAGTCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind9 CAAGCAGAAGACGGCATACGAGATCTGATCCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind10 CAAGCAGAAGACGGCATACGAGATAAGCTACTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind11 CAAGCAGAAGACGGCATACGAGATGTAGCCCTCGGCATTCCTGCTGAACCGCTCTT
PCR_R.N2Ind12 CAAGCAGAAGACGGCATACGAGATTACAAGCTCGGCATTCCTGCTGAACCGCTCTT
PCR_Fs AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC
N2IndSeq AAGAGCGGTTCAGCAGGAATGCCGAG
N2RevSeq(WRONG design) CTCGGCATTCCTGCTGAACCGCTCTT
N2RevSeq2 CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT

Nextera Read Primer

Sequence ID Sequence
Nextera Read 1 Primer 5'-GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGACAG-3'
Nextera Read 2 Primer 5'-GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGACAG-3'
Nextera Index Read Primer 5'-CTGTCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCG-3'