Revision as of 23:00, 11 June 2014 by >Dinh
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
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