Illumina GA/Oligo info
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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 | |||
- [1] Amplification-free Illumina sequencing-library preparation facilatates improved mapping and assembly of GC biased genomes
- [2] Improved protocols for the Illumina GA
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 |
Forward sequencing primer | SolSeqV6.3.2 | ACCGACACTCTCAGATGTTATCGAGGTCCGAC | None | None |
Reverse sequencing primer | SolSeqV6.3.2r | GCTAGGAACGATGAGCCTCCAAC | None | None |
Index read primer | AmpR6.3IndSeq | GTTGGAGGCTCATCGTTCCTAGC | None | None |
Forward extension primer | AmpF6.3SolExt | AATGATACGGCGACCACCGAGATCTACACCACTCTCAGATGTTATCGA | None | None |
Forward PCR primer | AmpF6.4Sol | AATGATACGGCGACCACCGAGATCTACACCACTCTCAGATGTTATCGAGGTCCGAC | None | None |
Forward sequencing primer | SolSeqV6.3.3 | TACACCACTCTCAGATGTTATCGAGGTCCGAC | None | None |
- The current version of sequencing primers used for Illumina’s PE flowcell
- SolSeq6.3.3 (read1) : (5’-TACACCACTCTCAGATGTTATCGAGGTCCGAC -3’)
- SolSeqV6.3.2r (read2) : (5’-GCTAGGAACGATGAGCCTCCAAC-3’)
- AmpR6.3IndSeq (Index read primer) : (5’-GTTGGAGGCTCATCGTTCCTAGC-3’)
- LibFreeIndSeqRev (Index read primer after 2nd strand synthesis) : (5’-CAAGCAGAAGACGGCATACGAGAT-3’)
- 48-plex primers designed by Dinh.
- Media:Library-free_BarcodeInfo384_designedbyDinh_June16_2011-edit.xls
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' |
Nextera Primer
ID | Sequence | Length |
Nextera Primer 1* | AATGATACGGCGACCACCGA | 20nt |
Nextera Primer 2* | CAAGCAGAAGACGGCATACGA | 21nt |
Nextera Adaptor 1* | AATGATACGGCGACCACCGAGATCTACACGCCTCCCTCGCGCCATCAG | 48nt |
Nextera Adaptor 2 (minus bar code)* | CAAGCAGAAGACGGCATACGAGATCGGTCTGCCTTGCCAGCCCGCTCAG | 49nt |
Orange primer | CCTTGCCAGCCCGCTCAG | 18nt |
Blue primer | CCTCCCTCGCGCCATCAG | 18nt |
Short Orange primer | CCTTGCCAGCC | 11nt |
Short Blue primer | CCTCCCTCGCG | 11nt |
Primers for LC Sciences probe experiment
Sequence ID | Sequnces | Length |
eMIP_CA1_F | TGCCTAGGACCGGATCAACT | 20 |
eMIP_CA1_R | GAGCTTCGGTTCACGCAATG | 20 |
CP-2-FA | GCACGATCCGACGGTAGTGT | 20 |
CP-2-RA | CCGTAATCGGGAAGCTGAAG | 20 |
CP-2-FA.IndSol | CAAGCAGAAGACGGCATACGAGATNNNNNNCGGTCTGCCATCCGACGGTAGTGT | 54 |
CP-2-RA.Sol | AATGATACGGCGACCACCGAGATCTACACGCCTATCGGGAAGCTGAAG | 48 |
Read 1: CP-2-SeqRead1.x | TACACGCCTATCGGGAAGCTGAAG | 24 |
Index Read: CP-2-IndSeq.x | ACACTACCGTCGGATGGCAGACCG | 24 |
Switch.CP-2-FA.Sol | AATGATACGGCGACCACCGAGATCTACACGCCTATCCGACGGTAGTGT | 48 |
Switch.CP-2-RA.IndSol | CAAGCAGAAGACGGCATACGAGATNNNNNNCGGTCTGCCATCGGGAAGCTGAAG | 54 |
Read 1 CP-2-SeqRead1.y | TACACGCCTATCCGACGGTAGTGT | 24 |
Index Read:CP-2-IndSeq.y | CTTCAGCTTCCCGATGGCAGACCG | 24 |