Illumina GA/Oligo info: Difference between revisions

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mNo edit summary
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| Indx80||verybad||TTACCA||GGTCTC
| Indx80||verybad||TTACCA||GGTCTC
|}
* Commercial barcodes with at least 1 base similarity:
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Barcode ID'''
| align="center" style="background:#f0f0f0;"|'''Barcode'''
| align="center" style="background:#f0f0f0;"|'''Related sequences'''
| align="center" style="background:#f0f0f0;"|'''Related sequences ID'''
|-
| Ada_Ind_1||CGTGAT||CGTGAT||Ind1,Ind1
|-
| Ada_Ind_2||ACATCG||ACATCG||Ind2,Ind2
|-
| Ada_Ind_3||GCCTAA||||
|-
| Ada_Ind_4||TGGTCA||TGGTCA||Ind4,Ind4
|-
| Ada_Ind_5||CACTGT||CACTGT||Ind5,Ind5
|-
| Ada_Ind_6||ATTGGC||ATTGGC||Ind6,Ind6
|-
| Ada_Ind_7||GATCTG||GATCTG||Ind7
|-
| Ada_Ind_8||TCAAGT||TCAAGT||Ind8
|-
| Ada_Ind_9||CTGATC||||
|-
| Ada_Ind_10||AAGCTA||AAGCTA||Ind10
|-
| Ada_Ind_11||GTAGCC||GTAGCC||Ind11
|-
| Ada_Ind_12||TACAAG||TACAAG||Ind12
|-
| Ada_Ind_13||TTGACT||||
|-
| Ada_Ind_14||GGAACT||TGAACT,GGCACT,GGATCT,GGAACG||Ind18,Ind43,Ind202,Ind294
|-
| Ada_Ind_15||TGACAT||TGCCAT||Ind271
|-
| Ada_Ind_16||GGACGG||GGACGT||Ind54
|-
| Ada_Ind_17||GCGGAC||TCGGAC,GCGGAA||Ind376,Ind284
|-
| Ada_Ind_18||TTTCAC||ATTCAC,TCTCAC,TTGCAC,TTTCTC||Ind353,Ind143,Ind150,Ind156
|-
| Ada_Ind_19||GGCCAC||GGCGAC,GACCAC||Ind72,Ind83
|-
| Ada_Ind_20||CGAAAC||GGAAAC,CGAGAC,CCAAAC,CGAAGC||Ind193,Ind253,Ind289,Ind293
|-
| Ada_Ind_21||CGTACG||||
|-
| Ada_Ind_22||CCACTC||CGACTC,CCAGTC||Ind3,Ind263
|-
| Ada_Ind_23||ATCAGT||ATCTGT||Ind60
|-
| Ada_Ind_24||AGGAAT||AGGAAG||Ind15
|-
| Ada_Ind_25||ATCAGT||ATCTGT||Ind60
|-
| Ada_Ind_27||AGGAAT||AGGAAG||Ind15
|-
| N701||GCCTTA||TCCTTA,GCCTTT||Ind110,Ind171
|-
| N702||AGTACG||||
|-
| N703||CTGCCT||CTGGCT||Ind252
|-
| N704||TCAGGA||TCACGA||Ind26
|-
| N705||GAGTCC||GAGTCC||Ind73
|-
| N706||TGCCTA||TGCCTA||Ind93
|-
| N707||AGAGAG||GGAGAG,ATAGAG,AGTGAG||Ind47,Ind61,Ind155
|-
| N708||TCTCTG||CCTCTG,TCGCTG||Ind364,Ind108
|-
| N709||CGTAGC||TGTAGC,CGTAGT,CGAAGC||Ind37,Ind45,Ind293
|-
| N710||GCCTCG||||
|-
| N711||CCTCTT||CCGCTT,CCTGTT,CCTCTG||Ind196,Ind211,Ind364
|-
| N712||CTCTAC||GTCTAC,CTATAC,CTCTAT,CGCTAC,CTCCAC||Ind375,Ind94,Ind200,Ind336,Ind339
|}
|}
* CURRENT: Primers master list [[File:ZhangLab_MultiplexingPrimers_BarcodeInfo384_06112014.xlsx]]
* CURRENT: Primers master list [[File:ZhangLab_MultiplexingPrimers_BarcodeInfo384_06112014.xlsx]]

Revision as of 23:00, 11 June 2014

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

Multiplexing Reverse PCR primers

  • Barcodes replaced:
IndexID MutationRate Old_sequence New_sequence
Indx03 verybad GCCTAA CGACTC
Indx09 verybad CTGATC GAGCTC
Indx32 verybad CCTTGC CAATTC
Indx50 verybad AAAGGT CCGCAC
Indx72 verybad TGGCAG GGCGAC
Indx80 verybad TTACCA GGTCTC
  • Commercial barcodes with at least 1 base similarity:
Barcode ID Barcode Related sequences Related sequences ID
Ada_Ind_1 CGTGAT CGTGAT Ind1,Ind1
Ada_Ind_2 ACATCG ACATCG Ind2,Ind2
Ada_Ind_3 GCCTAA
Ada_Ind_4 TGGTCA TGGTCA Ind4,Ind4
Ada_Ind_5 CACTGT CACTGT Ind5,Ind5
Ada_Ind_6 ATTGGC ATTGGC Ind6,Ind6
Ada_Ind_7 GATCTG GATCTG Ind7
Ada_Ind_8 TCAAGT TCAAGT Ind8
Ada_Ind_9 CTGATC
Ada_Ind_10 AAGCTA AAGCTA Ind10
Ada_Ind_11 GTAGCC GTAGCC Ind11
Ada_Ind_12 TACAAG TACAAG Ind12
Ada_Ind_13 TTGACT
Ada_Ind_14 GGAACT TGAACT,GGCACT,GGATCT,GGAACG Ind18,Ind43,Ind202,Ind294
Ada_Ind_15 TGACAT TGCCAT Ind271
Ada_Ind_16 GGACGG GGACGT Ind54
Ada_Ind_17 GCGGAC TCGGAC,GCGGAA Ind376,Ind284
Ada_Ind_18 TTTCAC ATTCAC,TCTCAC,TTGCAC,TTTCTC Ind353,Ind143,Ind150,Ind156
Ada_Ind_19 GGCCAC GGCGAC,GACCAC Ind72,Ind83
Ada_Ind_20 CGAAAC GGAAAC,CGAGAC,CCAAAC,CGAAGC Ind193,Ind253,Ind289,Ind293
Ada_Ind_21 CGTACG
Ada_Ind_22 CCACTC CGACTC,CCAGTC Ind3,Ind263
Ada_Ind_23 ATCAGT ATCTGT Ind60
Ada_Ind_24 AGGAAT AGGAAG Ind15
Ada_Ind_25 ATCAGT ATCTGT Ind60
Ada_Ind_27 AGGAAT AGGAAG Ind15
N701 GCCTTA TCCTTA,GCCTTT Ind110,Ind171
N702 AGTACG
N703 CTGCCT CTGGCT Ind252
N704 TCAGGA TCACGA Ind26
N705 GAGTCC GAGTCC Ind73
N706 TGCCTA TGCCTA Ind93
N707 AGAGAG GGAGAG,ATAGAG,AGTGAG Ind47,Ind61,Ind155
N708 TCTCTG CCTCTG,TCGCTG Ind364,Ind108
N709 CGTAGC TGTAGC,CGTAGT,CGAAGC Ind37,Ind45,Ind293
N710 GCCTCG
N711 CCTCTT CCGCTT,CCTGTT,CCTCTG Ind196,Ind211,Ind364
N712 CTCTAC GTCTAC,CTATAC,CTCTAT,CGCTAC,CTCCAC Ind375,Ind94,Ind200,Ind336,Ind339

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

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
N2FwdSeq2H (for overloaded flowcells only) CACTCTTTCCCTACACGACGCTCTTCCGATCTH
N2RevSeq2H (for overloaded flowcells only) TCGGCATTCCTGCTGAACCGCTCTTCCGATCTH

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 BSPP probes synthesized by Agilent

Sequence ID Sequences Length
pAP1V61U 5’-G*G*G*TCATATCGGTCACTGTU-3’ 18
AP1V6 5\'- GTCATATCGGTCACTGTT -3\' 18
AP2V6 5’-/5Phos/CACGGGTAGTGTGTATCCTG-3’ 20
  • * Indicates a phosphorothioate bond

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


Primers for LC Sciences library-free protocol

Sequence ID Sequences Length
CA-2-FA.Indx7Sol 5’-CAAGCAGAAGACGGCATACGAGATGATCTGCGGTCTGCCATCCGACGGTAGTGT-3’ 54
CA-2-FA.Indx45Sol 5'-CAAGCAGAAGACGGCATACGAGATCGTAGTCGGTCTGCCATCCGACGGTAGTGT-3' 54
CA-2-FA.Indx76Sol 5'-CAAGCAGAAGACGGCATACGAGATAATAGGCGGTCTGCCATCCGACGGTAGTGT-3' 54
CA-2-FA.Indx77Sol 5'-CAAGCAGAAGACGGCATACGAGATACCCGTCGGTCTGCCATCCGACGGTAGTGT-3' 54
CA-2-FA.Indx78Sol 5'-CAAGCAGAAGACGGCATACGAGATAACACGCGGTCTGCCATCCGACGGTAGTGT-3' 54
CA-2-RA.Sol 5’-AATGATACGGCGACCACCGAGATCTACACGCCTATCGGGAAGCTGAAG-3’ 48
CP-2-SeqRead1.x (Read1) 5’-TACACGCCTATCGGGAAGCTGAAG-3’ 24
CP-2-SeqRead2 5'-CGGTCTGCCATCCGACGGTAGTGT-3' 24
CP-2-IndSeq.x (IndexRead) 5’-ACACTACCGTCGGATGGCAGACCG-3’ 24


Primers for totoRNAseq protocol

STRT-SEQ Read 1 v3

GATCTAAGCAGTGGTATCAACGCAGAGTACGGG
33nt   Tm=71.2 (Kun's)
correspond to TSO.r06 used for 5'end

totoRNAseq Read 1: [1]

CACCGAGATCTACACTCTTTCCCTACACGACGTT
34nt 	Tm=64(IDT)	Tm=71.72(Kun's)
correspond to TSO.idXX primers used for 5'end

totoRNAseq Read 1 v2:

CCACCGAGATCTACACTCTTTCCCTACACGACG
33nt 	Tm=64.5(IDT)	Tm=72.04(Kun's)
correspond to TSO.r02/TSO.r04 primers used for 5'end

RL.T7.IndSeq:

AAAAAAAAAAAAAAAAAAAAGCGGGCTGGCAAGG
34nt 	Tm=60.7(IDT)	Tm=68.5(Kun's)
correspond to RL.T7.id01-24 primers used for RT step (T20 based primers)

Primers for NEBNext Multiplex Oligos (updated May 08, 2013)

NEBNext adaptor for Illumina: 5´-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC/ideoxyu/ACACTCTTTCCCT ACACGACGCTCTTCCGATC*T-3´ (loop adaptor, commercially purchased for ultra-low input ligation)
Sequence ID Sequences
NEBNext Universal PCR Primer (PCR_F) 5´-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC-s-T-3´
NEBNext Index 1 5´-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 2 5´-CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 3 5´-CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 4 5´-CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 5 5´-CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 6 5´-CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3'
NEBNext Index 7 5´-CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 8 5´-CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 9 5´-CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 10 5´-CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 11 5´-CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
NEBNext Index 12 5´-CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-s-T-3´
HP1 -> updated to HP6 (read1)
NEBNextRevSeq2 (read2) 5' -GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT- 3'
NEBNextIndSeq (index read) 5' -GAAGAGCACACGTCTGAACTCCAGTCAC- 3'

HiTSFLIP Sequencing Primer

  • HiTSFLIP SEQ 1 5'GATCACGACGCTCTTCCGATCTCTACACTCTTTCCCTA
  • Multiplexing Index Read Sequencing Primer 5' GATCGGAAGAGCACACGTCTGAACTCCAGTCAC

Adaptors/Primers for RRBS experiment, (updated Apr 24, 2014)

Barcoded adaptors

Name in Illumin TrueSeq Sequences (5'-->3')
TruSeq Universal Adapter 5'- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -3'
TruSeq Adapter, Index XX 5'- GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3'

PCR primers

TruS_F 5'- AATGATACGGCGACCACCGAGATC -3' Tm = 67.1 C
TruS_R 5'- CAAGCAGAAGACGGCATACGAGAT -3' Tm = 65.5 C

Read1: HP10
Index read:HP12
Read2: HP11