Illumina GA/Oligo info: Difference between revisions

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==Indexes for Library Submission==
[https://docs.google.com/spreadsheets/d/1F2L2NpqYCXYwYPk1WQdJDkj3yZKMJftYfeYUHtiXCL4/pubhtml#]
{| {{table}}
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Name in original paper'''
| align="center" style="background:#f0f0f0;"|'''Name in original paper'''
Line 55: Line 57:


==Multiplexing Reverse PCR primers==
==Multiplexing Reverse PCR primers==
* Primer list and assigned managers [[File:ZhangLab_MultiplexingPrimers_BarcodeInfo384_12212011.xls]]
* Barcodes replaced:
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''IndexID'''
| align="center" style="background:#f0f0f0;"|'''MutationRate'''
| align="center" style="background:#f0f0f0;"|'''Old_sequence'''
| align="center" style="background:#f0f0f0;"|'''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 more than 4 bases similarity with ours:
{| 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'''
|-
| TruSeq_Ind_1||CGTGAT||CGTGAT||Ind1
|-
| TruSeq_Ind_2||ACATCG||ACATCG||Ind2
|-
| TruSeq_Ind_3||GCCTAA||||
|-
| TruSeq_Ind_4||TGGTCA||TGGTCA||Ind4
|-
| TruSeq_Ind_5||CACTGT||CACTGT||Ind5
|-
| TruSeq_Ind_6||ATTGGC||ATTGGC||Ind6
|-
| TruSeq_Ind_7||GATCTG||GATCTG||Ind7
|-
| TruSeq_Ind_8||TCAAGT||TCAAGT||Ind8
|-
| TruSeq_Ind_9||CTGATC||||
|-
| TruSeq_Ind_10||AAGCTA||AAGCTA||Ind10
|-
| TruSeq_Ind_11||GTAGCC||GTAGCC||Ind11
|-
| TruSeq_Ind_12||TACAAG||TACAAG||Ind12
|-
| TruSeq_Ind_13||TTGACT||||
|-
| TruSeq_Ind_14||GGAACT||TGAACT,GGCACT,GGATCT,GGAACG||Ind18,Ind43,Ind202,Ind294
|-
| TruSeq_Ind_15||TGACAT||TGCCAT||Ind271
|-
| TruSeq_Ind_16||GGACGG||GGACGT||Ind54
|-
| TruSeq_Ind_18||GCGGAC||TCGGAC,GCGGAA||Ind376,Ind284
|-
| TruSeq_Ind_19||TTTCAC||ATTCAC,TCTCAC,TTGCAC,TTTCTC||Ind353,Ind143,Ind150,Ind156
|-
| TruSeq_Ind_20||GGCCAC||GGCGAC,GACCAC||Ind72,Ind83
|-
| TruSeq_Ind_21||CGAAAC||GGAAAC,CGAGAC,CCAAAC,CGAAGC||Ind193,Ind253,Ind289,Ind293
|-
| TruSeq_Ind_22||CGTACG||||
|-
| TruSeq_Ind_23||CCACTC||CGACTC,CCAGTC||Ind3,Ind263
|-
| TruSeq_Ind_25||ATCAGT||ATCTGT||Ind60
|-
| TruSeq_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]]
* Primers master list old [[File:ZhangLab_MultiplexingPrimers_BarcodeInfo384_12212011.xls]]
 
==Library Free Multiplexing Primers for Dual-Index==
* Sequencing primers: ALL CUSTOM PRIMERS (except i5 read primer is the same as standard)
**PE Read 1 Sequencing Primer: 5' TGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC (Tm = 79.93 C)
**PE Read 2 Sequencing Primer: 5' AGGAGTTCGGCTAGGAACGATGAGCCTCCAAC (Tm = 79.15 C)
**Multiplexing Read 1 Sequencing Primer (i7): 5' GTTGGAGGCTCATCGTTCCTAGCCGAACTCCT (Tm = 79.15 C)
**Multiplexing Read 2 Sequencing Primer (i5): 5' AATGATACGGCGACCACCGAGATCTACAC (Tm = 74.60 C)
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Name'''
| align="center" style="background:#f0f0f0;"|'''Nick-name'''
| align="center" style="background:#f0f0f0;"|'''Barcode'''
| align="center" style="background:#f0f0f0;"|'''Barcode sequence sample sheet'''
| align="center" style="background:#f0f0f0;"|'''Sequence (5\'->3\')'''
| align="center" style="background:#f0f0f0;"|'''Length'''
|-
| AmpF7.S502||S502||CTCTCTAT||CTCTCTAT||AATGATACGGCGACCACCGAGATCTACACCTCTCTATTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S503||S503||TATCCTCT||TATCCTCT||AATGATACGGCGACCACCGAGATCTACACTATCCTCTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S505||S505||GTAAGGAG||GTAAGGAG||AATGATACGGCGACCACCGAGATCTACACGTAAGGAGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S506||S506||ACTGCATA||ACTGCATA||AATGATACGGCGACCACCGAGATCTACACACTGCATATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S507||S507||AAGGAGTA||AAGGAGTA||AATGATACGGCGACCACCGAGATCTACACAAGGAGTATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S508||S508||CTAAGCCT||CTAAGCCT||AATGATACGGCGACCACCGAGATCTACACCTAAGCCTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S510||S510||CGTCTAAT||CGTCTAAT||AATGATACGGCGACCACCGAGATCTACACCGTCTAATTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S511||S511||TCTCTCCG||TCTCTCCG||AATGATACGGCGACCACCGAGATCTACACTCTCTCCGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S513||S513||TCGACTAG||TCGACTAG||AATGATACGGCGACCACCGAGATCTACACTCGACTAGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S515||S515||TTCTAGCT||TTCTAGCT||AATGATACGGCGACCACCGAGATCTACACTTCTAGCTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S516||S516||CCTAGAGT||CCTAGAGT||AATGATACGGCGACCACCGAGATCTACACCCTAGAGTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S517||S517||GCGTAAGA||GCGTAAGA||AATGATACGGCGACCACCGAGATCTACACGCGTAAGATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S518||S518||CTATTAAG||CTATTAAG||AATGATACGGCGACCACCGAGATCTACACCTATTAAGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S520||S520||AAGGCTAT||AAGGCTAT||AATGATACGGCGACCACCGAGATCTACACAAGGCTATTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S521||S521||GAGCCTTA||GAGCCTTA||AATGATACGGCGACCACCGAGATCTACACGAGCCTTATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|-
| AmpF7.S522||S522||TTATGCGA||TTATGCGA||AATGATACGGCGACCACCGAGATCTACACTTATGCGATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC||73
|}
{| class="wikitable"
| align="center" style="background:#f0f0f0;"|'''Name'''
| align="center" style="background:#f0f0f0;"|'''Nick-name'''
| align="center" style="background:#f0f0f0;"|'''Barcode'''
| align="center" style="background:#f0f0f0;"|'''Barcode sequence sample sheet'''
| align="center" style="background:#f0f0f0;"|'''Sequence (5\'->3\')'''
| align="center" style="background:#f0f0f0;"|'''Length'''
|-
| AmpR7.N701||N701||TCGCCTTA||TAAGGCGA||CAAGCAGAAGACGGCATACGAGATTCGCCTTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N702||N702||CTAGTACG||CGTACTAG||CAAGCAGAAGACGGCATACGAGATCTAGTACGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N703||N703||TTCTGCCT||AGGCAGAA||CAAGCAGAAGACGGCATACGAGATTTCTGCCTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N704||N704||GCTCAGGA||TCCTGAGC||CAAGCAGAAGACGGCATACGAGATGCTCAGGAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N705||N705||AGGAGTCC||GGACTCCT||CAAGCAGAAGACGGCATACGAGATAGGAGTCCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N706||N706||CATGCCTA||TAGGCATG||CAAGCAGAAGACGGCATACGAGATCATGCCTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N707||N707||GTAGAGAG||CTCTCTAC||CAAGCAGAAGACGGCATACGAGATGTAGAGAGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N710||N710||CAGCCTCG||CGAGGCTG||CAAGCAGAAGACGGCATACGAGATCAGCCTCGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N711||N711||TGCCTCTT||AAGAGGCA||CAAGCAGAAGACGGCATACGAGATTGCCTCTTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N712||N712||TCCTCTAC||GTAGAGGA||CAAGCAGAAGACGGCATACGAGATTCCTCTACAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N714||N714||TCATGAGC||GCTCATGA||CAAGCAGAAGACGGCATACGAGATTCATGAGCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N715||N715||CCTGAGAT||ATCTCAGG||CAAGCAGAAGACGGCATACGAGATCCTGAGATAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N716||N716||TAGCGAGT||ACTCGCTA||CAAGCAGAAGACGGCATACGAGATTAGCGAGTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N718||N718||GTAGCTCC||GGAGCTAC||CAAGCAGAAGACGGCATACGAGATGTAGCTCCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N719||N719||TACTACGC||GCGTAGTA||CAAGCAGAAGACGGCATACGAGATTACTACGCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N720||N720||AGGCTCCG||CGGAGCCT||CAAGCAGAAGACGGCATACGAGATAGGCTCCGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N721||N721||GCAGCGTA||TACGCTGC||CAAGCAGAAGACGGCATACGAGATGCAGCGTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N722||N722||CTGCGCAT||ATGCGCAG||CAAGCAGAAGACGGCATACGAGATCTGCGCATAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N723||N723||GAGCGCTA||TAGCGCTC||CAAGCAGAAGACGGCATACGAGATGAGCGCTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N724||N724||CGCTCAGT||ACTGAGCG||CAAGCAGAAGACGGCATACGAGATCGCTCAGTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N726||N726||GTCTTAGG||CCTAAGAC||CAAGCAGAAGACGGCATACGAGATGTCTTAGGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N727||N727||ACTGATCG||CGATCAGT||CAAGCAGAAGACGGCATACGAGATACTGATCGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N728||N728||TAGCTGCA||TGCAGCTA||CAAGCAGAAGACGGCATACGAGATTAGCTGCAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|-
| AmpR7.N729||N729||GACGTCGA||TCGACGTC||CAAGCAGAAGACGGCATACGAGATGACGTCGAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC||64
|}


==Library Free Multiplexing Primers==
==Library Free Multiplexing Primers==
Line 236: Line 440:
| Index Read:CP-2-IndSeq.y||CTTCAGCTTCCCGATGGCAGACCG||24
| Index Read:CP-2-IndSeq.y||CTTCAGCTTCCCGATGGCAGACCG||24
|}<br>
|}<br>
== Primer for LC Sciences library-free protocol ==
== Primers for LC Sciences library-free protocol ==
* [[http://genome-tech.ucsd.edu/LabNotes/upload/2/2f/LC_Sciences_DMR_Probes_Design.pdf  Scheme of LC Sciences probe design]]
{| {{table}}
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Sequence ID'''
| align="center" style="background:#f0f0f0;"|'''Sequence ID'''
Line 244: Line 449:
| CA-2-FA.Indx7Sol||5’-CAAGCAGAAGACGGCATACGAGATGATCTGCGGTCTGCCATCCGACGGTAGTGT-3’||54
| CA-2-FA.Indx7Sol||5’-CAAGCAGAAGACGGCATACGAGATGATCTGCGGTCTGCCATCCGACGGTAGTGT-3’||54
|-
|-
| CA-2-FA.Indx45Sol||5\'-CAAGCAGAAGACGGCATACGAGATCGTAGTCGGTCTGCCATCCGACGGTAGTGT-3\'||54
| CA-2-FA.Indx45Sol||5'-CAAGCAGAAGACGGCATACGAGATCGTAGTCGGTCTGCCATCCGACGGTAGTGT-3'||54
|-
|-
| CA-2-FA.Indx76Sol||5\'-CAAGCAGAAGACGGCATACGAGATAATAGGCGGTCTGCCATCCGACGGTAGTGT-3\'||54
| CA-2-FA.Indx76Sol||5'-CAAGCAGAAGACGGCATACGAGATAATAGGCGGTCTGCCATCCGACGGTAGTGT-3'||54
|-
|-
| CA-2-FA.Indx77Sol||5\'-CAAGCAGAAGACGGCATACGAGATACCCGTCGGTCTGCCATCCGACGGTAGTGT-3\'||54
| CA-2-FA.Indx77Sol||5'-CAAGCAGAAGACGGCATACGAGATACCCGTCGGTCTGCCATCCGACGGTAGTGT-3'||54
|-
|-
| CA-2-FA.Indx78Sol ||5\'-CAAGCAGAAGACGGCATACGAGATAACACGCGGTCTGCCATCCGACGGTAGTGT-3\'||54
| CA-2-FA.Indx78Sol||5'-CAAGCAGAAGACGGCATACGAGATAACACGCGGTCTGCCATCCGACGGTAGTGT-3'||54
|-
|-
| CA-2-RA.Sol||5’-AATGATACGGCGACCACCGAGATCTACACGCCTATCGGGAAGCTGAAG-3’||48
| CA-2-RA.Sol||5’-AATGATACGGCGACCACCGAGATCTACACGCCTATCGGGAAGCTGAAG-3’||48
|-
|-
| CP-2-SeqRead1.x (Read1) ||5’-TACACGCCTATCGGGAAGCTGAAG-3’||24
| 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: [http://genome-tech.ucsd.edu/LabNotes/index.php/Rui:LabNotes/SingleCell/2012-10-30#Sequencing_primer_design]
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) ==
* Reference: [https://www.neb.com/~/media/Catalog/All-Products/33E45F5CD69B497E92C1073F5D551DC7/Datacards%20or%20Manuals/manualE7335.pdf]
{| {{table}}
| NEBNext adaptor for Illumina:||5´-/5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTC/ideoxyu/ACACTCTTTCCCT ACACGACGCTCTTCCGATC*T-3´ (loop adaptor, commercially purchased for ultra-low input ligation)
|}
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Sequence ID'''
| align="center" style="background:#f0f0f0;"|'''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'
|}
* '''-s-''' = phosphorothioate bond
* May 2013, more NEBNext Index primers (Index 9-32) in 96-well plate were ordered. The new primers do not have phosphorothioate bond at -s-T-3´ end as the ones from NEB kit.
* Updated [[Media:ZhangLab_NEBNext_MultiplexingPrimers_BarcodeInfo_06142013.xlsx| ZhangLab_NEBNext_MultiplexingPrimers_BarcodeInfo_06142013]]
==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'''<br>
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Name in Illumina TrueSeq kit'''
| align="center" style="background:#f0f0f0;"|'''Sequences (5'-->3')'''
|-
| TruSeq Universal Adapter||5'- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -3'
|-
| TruSeq Adapter, Index XX||5'- GATCGGAAGAGCACACGTCTGAACTCCAGTCAC<u>NNNNNN</u>ATCTCGTATGCCGTCTTCTGCTTG -3'
|}
* Note:
** TruSeq adaptor barcode Index 1-12 are the same as Zhanglab's Index 1-96, but Index13-27 are different as list below.
** Index numbers 17, 24, and 26 are reserved by Illumina.
{| {{table}}
| align="center" style="width:120px;background:#f0f0f0;"|'''Index'''
| align="center" style="width:140px;background:#f0f0f0;"|'''Barcodes'''
|-
| TruSeq_Ind13||AGTCAA
|-
| TruSeq_Ind14||AGTTCC
|-
| TruSeq_Ind15||ATGTCA
|-
| TruSeq_Ind16||CCGTCC
|-
| TruSeq_Ind18||GTCCGC
|-
| TruSeq_Ind19||GTGAAA
|-
| TruSeq_Ind20||GTGGCC
|-
| TruSeq_Ind21||GTTTCG
|-
| TruSeq_Ind22||CGTACG
|-
| TruSeq_Ind23||GAGTGG
|-
| TruSeq_Ind25||ACTGAT
|-
| TruSeq_Ind27||ATTCCT
|}
''' PCR primers'''
{| {{table}}
|  TruS_F||5'- AATGATACGGCGACCACCGAGATC -3'||Tm = 67.1 C
|-
| TruS_R||5'- CAAGCAGAAGACGGCATACGAGAT -3'||Tm = 65.5 C
|}
'''Read1:'''  HP10<br>
'''Index read:'''HP12<br>
'''Read2:''' HP11
 
==Sten's EZ-Tn5 protocol related primers==
C1-P1-PCR-2 /5Biosg/GAATGATACGGCGACCACCGAT
C1-TN5-U /5Phos/CTGTCTCTTATACACATCTGACGC
 
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Order'''
| align="center" style="background:#f0f0f0;"|'''Barcode'''
| align="center" style="background:#f0f0f0;"|'''Name'''
| align="center" style="background:#f0f0f0;"|'''Sequence'''
|-
| 1||CGTCTAAT||C1-TN5-1||CAAGCAGAAGACGGCATACGACGTCTAATGCGTCAGATGTGTATAAGAGACAG
|-
| 2||AGACTCGT||C1-TN5-2||CAAGCAGAAGACGGCATACGAAGACTCGTGCGTCAGATGTGTATAAGAGACAG
|-
| 3||GCACGTCA||C1-TN5-3||CAAGCAGAAGACGGCATACGAGCACGTCAGCGTCAGATGTGTATAAGAGACAG
|-
| 4||TCAACGAC||C1-TN5-4||CAAGCAGAAGACGGCATACGATCAACGACGCGTCAGATGTGTATAAGAGACAG
|-
| 5||ATTTAGCG||C1-TN5-5||CAAGCAGAAGACGGCATACGAATTTAGCGGCGTCAGATGTGTATAAGAGACAG
|-
| 6||ATACAGAC||C1-TN5-6||CAAGCAGAAGACGGCATACGAATACAGACGCGTCAGATGTGTATAAGAGACAG
|-
| 7||TGCGTAGG||C1-TN5-7||CAAGCAGAAGACGGCATACGATGCGTAGGGCGTCAGATGTGTATAAGAGACAG
|-
| 8||TGGAGCTC||C1-TN5-8||CAAGCAGAAGACGGCATACGATGGAGCTCGCGTCAGATGTGTATAAGAGACAG
|-
| 9||TGAATACC||C1-TN5-9||CAAGCAGAAGACGGCATACGATGAATACCGCGTCAGATGTGTATAAGAGACAG
|-
| 10||TCTCACAC||C1-TN5-10||CAAGCAGAAGACGGCATACGATCTCACACGCGTCAGATGTGTATAAGAGACAG
|-
| 11||TACTGGTA||C1-TN5-11||CAAGCAGAAGACGGCATACGATACTGGTAGCGTCAGATGTGTATAAGAGACAG
|-
| 12||ACGATAGG||C1-TN5-12||CAAGCAGAAGACGGCATACGAACGATAGGGCGTCAGATGTGTATAAGAGACAG
|-
| 13||GATGTCGA||C1-TN5-13||CAAGCAGAAGACGGCATACGAGATGTCGAGCGTCAGATGTGTATAAGAGACAG
|-
| 14||TTACGGGT||C1-TN5-14||CAAGCAGAAGACGGCATACGATTACGGGTGCGTCAGATGTGTATAAGAGACAG
|-
| 15||CACAGCAT||C1-TN5-15||CAAGCAGAAGACGGCATACGACACAGCATGCGTCAGATGTGTATAAGAGACAG
|-
| 16||CTTTGACA||C1-TN5-16||CAAGCAGAAGACGGCATACGACTTTGACAGCGTCAGATGTGTATAAGAGACAG
|-
| 17||CCTTCAAG||C1-TN5-17||CAAGCAGAAGACGGCATACGACCTTCAAGGCGTCAGATGTGTATAAGAGACAG
|-
| 18||GAGTCCTG||C1-TN5-18||CAAGCAGAAGACGGCATACGAGAGTCCTGGCGTCAGATGTGTATAAGAGACAG
|-
| 19||CACACTGA||C1-TN5-19||CAAGCAGAAGACGGCATACGACACACTGAGCGTCAGATGTGTATAAGAGACAG
|-
| 20||GTTACAGG||C1-TN5-20||CAAGCAGAAGACGGCATACGAGTTACAGGGCGTCAGATGTGTATAAGAGACAG
|-
| 21||GGACCTTT||C1-TN5-21||CAAGCAGAAGACGGCATACGAGGACCTTTGCGTCAGATGTGTATAAGAGACAG
|-
| 22||TTCCGTTC||C1-TN5-22||CAAGCAGAAGACGGCATACGATTCCGTTCGCGTCAGATGTGTATAAGAGACAG
|-
| 23||ACTGTTTG||C1-TN5-23||CAAGCAGAAGACGGCATACGAACTGTTTGGCGTCAGATGTGTATAAGAGACAG
|-
| 24||AAGTGGCT||C1-TN5-24||CAAGCAGAAGACGGCATACGAAAGTGGCTGCGTCAGATGTGTATAAGAGACAG
|-
| 25||CTGTACAA||C1-TN5-25||CAAGCAGAAGACGGCATACGACTGTACAAGCGTCAGATGTGTATAAGAGACAG
|-
| 26||CGCAAAGT||C1-TN5-26||CAAGCAGAAGACGGCATACGACGCAAAGTGCGTCAGATGTGTATAAGAGACAG
|-
| 27||GTGCATGA||C1-TN5-27||CAAGCAGAAGACGGCATACGAGTGCATGAGCGTCAGATGTGTATAAGAGACAG
|-
| 28||GTCATTAG||C1-TN5-28||CAAGCAGAAGACGGCATACGAGTCATTAGGCGTCAGATGTGTATAAGAGACAG
|-
| 29||AGCTCCTT||C1-TN5-29||CAAGCAGAAGACGGCATACGAAGCTCCTTGCGTCAGATGTGTATAAGAGACAG
|-
| 30||TCACCCGA||C1-TN5-30||CAAGCAGAAGACGGCATACGATCACCCGAGCGTCAGATGTGTATAAGAGACAG
|-
| 31||GTTGCCAC||C1-TN5-31||CAAGCAGAAGACGGCATACGAGTTGCCACGCGTCAGATGTGTATAAGAGACAG
|-
| 32||TGTACCAA||C1-TN5-32||CAAGCAGAAGACGGCATACGATGTACCAAGCGTCAGATGTGTATAAGAGACAG
|-
| 33||AACGAGGT||C1-TN5-33||CAAGCAGAAGACGGCATACGAAACGAGGTGCGTCAGATGTGTATAAGAGACAG
|-
| 34||AGCCACCA||C1-TN5-34||CAAGCAGAAGACGGCATACGAAGCCACCAGCGTCAGATGTGTATAAGAGACAG
|-
| 35||GGTAATCA||C1-TN5-35||CAAGCAGAAGACGGCATACGAGGTAATCAGCGTCAGATGTGTATAAGAGACAG
|-
| 36||CCAGTCCA||C1-TN5-36||CAAGCAGAAGACGGCATACGACCAGTCCAGCGTCAGATGTGTATAAGAGACAG
|-
| 37||ACCTCAGC||C1-TN5-37||CAAGCAGAAGACGGCATACGAACCTCAGCGCGTCAGATGTGTATAAGAGACAG
|-
| 38||GGTGGACT||C1-TN5-38||CAAGCAGAAGACGGCATACGAGGTGGACTGCGTCAGATGTGTATAAGAGACAG
|-
| 39||GACAAACC||C1-TN5-39||CAAGCAGAAGACGGCATACGAGACAAACCGCGTCAGATGTGTATAAGAGACAG
|-
| 40||TAACTCCG||C1-TN5-40||CAAGCAGAAGACGGCATACGATAACTCCGGCGTCAGATGTGTATAAGAGACAG
|-
| 41||ACACCGTG||C1-TN5-41||CAAGCAGAAGACGGCATACGAACACCGTGGCGTCAGATGTGTATAAGAGACAG
|-
| 42||GTAGAACG||C1-TN5-42||CAAGCAGAAGACGGCATACGAGTAGAACGGCGTCAGATGTGTATAAGAGACAG
|-
| 43||GGATTGAC||C1-TN5-43||CAAGCAGAAGACGGCATACGAGGATTGACGCGTCAGATGTGTATAAGAGACAG
|-
| 44||ACGTATCC||C1-TN5-44||CAAGCAGAAGACGGCATACGAACGTATCCGCGTCAGATGTGTATAAGAGACAG
|-
| 45||TTCGGAAA||C1-TN5-45||CAAGCAGAAGACGGCATACGATTCGGAAAGCGTCAGATGTGTATAAGAGACAG
|-
| 46||AGTTGTGT||C1-TN5-46||CAAGCAGAAGACGGCATACGAAGTTGTGTGCGTCAGATGTGTATAAGAGACAG
|-
| 47||AAGCACAT||C1-TN5-47||CAAGCAGAAGACGGCATACGAAAGCACATGCGTCAGATGTGTATAAGAGACAG
|-
| 48||CTGTCATT||C1-TN5-48||CAAGCAGAAGACGGCATACGACTGTCATTGCGTCAGATGTGTATAAGAGACAG
|-
| 49||GTCCTATA||C1-TN5-49||CAAGCAGAAGACGGCATACGAGTCCTATAGCGTCAGATGTGTATAAGAGACAG
|-
| 50||CTACGCTG||C1-TN5-50||CAAGCAGAAGACGGCATACGACTACGCTGGCGTCAGATGTGTATAAGAGACAG
|-
| 51||GGGATTGT||C1-TN5-51||CAAGCAGAAGACGGCATACGAGGGATTGTGCGTCAGATGTGTATAAGAGACAG
|-
| 52||TGATGTAG||C1-TN5-52||CAAGCAGAAGACGGCATACGATGATGTAGGCGTCAGATGTGTATAAGAGACAG
|-
| 53||TTCGCTGT||C1-TN5-53||CAAGCAGAAGACGGCATACGATTCGCTGTGCGTCAGATGTGTATAAGAGACAG
|-
| 54||GAAGACTT||C1-TN5-54||CAAGCAGAAGACGGCATACGAGAAGACTTGCGTCAGATGTGTATAAGAGACAG
|-
| 55||TCTGGGCA||C1-TN5-55||CAAGCAGAAGACGGCATACGATCTGGGCAGCGTCAGATGTGTATAAGAGACAG
|-
| 56||CAACTAGA||C1-TN5-56||CAAGCAGAAGACGGCATACGACAACTAGAGCGTCAGATGTGTATAAGAGACAG
|-
| 57||CCATGGGA||C1-TN5-57||CAAGCAGAAGACGGCATACGACCATGGGAGCGTCAGATGTGTATAAGAGACAG
|-
| 58||ATGCGACG||C1-TN5-58||CAAGCAGAAGACGGCATACGAATGCGACGGCGTCAGATGTGTATAAGAGACAG
|-
| 59||GAGGGTAG||C1-TN5-59||CAAGCAGAAGACGGCATACGAGAGGGTAGGCGTCAGATGTGTATAAGAGACAG
|-
| 60||CGGGTGAA||C1-TN5-60||CAAGCAGAAGACGGCATACGACGGGTGAAGCGTCAGATGTGTATAAGAGACAG
|-
| 61||GCCATCTT||C1-TN5-61||CAAGCAGAAGACGGCATACGAGCCATCTTGCGTCAGATGTGTATAAGAGACAG
|-
| 62||GCATAATC||C1-TN5-62||CAAGCAGAAGACGGCATACGAGCATAATCGCGTCAGATGTGTATAAGAGACAG
|-
| 63||TCTATGGT||C1-TN5-63||CAAGCAGAAGACGGCATACGATCTATGGTGCGTCAGATGTGTATAAGAGACAG
|-
| 64||AGGACTTA||C1-TN5-64||CAAGCAGAAGACGGCATACGAAGGACTTAGCGTCAGATGTGTATAAGAGACAG
|-
| 65||CGTGATTC||C1-TN5-65||CAAGCAGAAGACGGCATACGACGTGATTCGCGTCAGATGTGTATAAGAGACAG
|-
| 66||ACTAGCGA||C1-TN5-66||CAAGCAGAAGACGGCATACGAACTAGCGAGCGTCAGATGTGTATAAGAGACAG
|-
| 67||GTAACTCC||C1-TN5-67||CAAGCAGAAGACGGCATACGAGTAACTCCGCGTCAGATGTGTATAAGAGACAG
|-
| 68||CGGAAGTG||C1-TN5-68||CAAGCAGAAGACGGCATACGACGGAAGTGGCGTCAGATGTGTATAAGAGACAG
|-
| 69||CCGAGTAC||C1-TN5-69||CAAGCAGAAGACGGCATACGACCGAGTACGCGTCAGATGTGTATAAGAGACAG
|-
| 70||GACGCAAT||C1-TN5-70||CAAGCAGAAGACGGCATACGAGACGCAATGCGTCAGATGTGTATAAGAGACAG
|-
| 71||ACCTGGAG||C1-TN5-71||CAAGCAGAAGACGGCATACGAACCTGGAGGCGTCAGATGTGTATAAGAGACAG
|-
| 72||CATGGGTT||C1-TN5-72||CAAGCAGAAGACGGCATACGACATGGGTTGCGTCAGATGTGTATAAGAGACAG
|-
| 73||ATTCCTAG||C1-TN5-73||CAAGCAGAAGACGGCATACGAATTCCTAGGCGTCAGATGTGTATAAGAGACAG
|-
| 74||AATCATGC||C1-TN5-74||CAAGCAGAAGACGGCATACGAAATCATGCGCGTCAGATGTGTATAAGAGACAG
|-
| 75||GCTTCCCT||C1-TN5-75||CAAGCAGAAGACGGCATACGAGCTTCCCTGCGTCAGATGTGTATAAGAGACAG
|-
| 76||AGGTAAAG||C1-TN5-76||CAAGCAGAAGACGGCATACGAAGGTAAAGGCGTCAGATGTGTATAAGAGACAG
|-
| 77||CCACAACT||C1-TN5-77||CAAGCAGAAGACGGCATACGACCACAACTGCGTCAGATGTGTATAAGAGACAG
|-
| 78||ACAGGCAT||C1-TN5-78||CAAGCAGAAGACGGCATACGAACAGGCATGCGTCAGATGTGTATAAGAGACAG
|-
| 79||TTTGTGTC||C1-TN5-79||CAAGCAGAAGACGGCATACGATTTGTGTCGCGTCAGATGTGTATAAGAGACAG
|-
| 80||TGAGCATA||C1-TN5-80||CAAGCAGAAGACGGCATACGATGAGCATAGCGTCAGATGTGTATAAGAGACAG
|-
| 81||TTAGACGC||C1-TN5-81||CAAGCAGAAGACGGCATACGATTAGACGCGCGTCAGATGTGTATAAGAGACAG
|-
| 82||CGCTTGCT||C1-TN5-82||CAAGCAGAAGACGGCATACGACGCTTGCTGCGTCAGATGTGTATAAGAGACAG
|-
| 83||AGTCTGCC||C1-TN5-83||CAAGCAGAAGACGGCATACGAAGTCTGCCGCGTCAGATGTGTATAAGAGACAG
|-
| 84||CATAGTCG||C1-TN5-84||CAAGCAGAAGACGGCATACGACATAGTCGGCGTCAGATGTGTATAAGAGACAG
|-
| 85||TCTTGCTG||C1-TN5-85||CAAGCAGAAGACGGCATACGATCTTGCTGGCGTCAGATGTGTATAAGAGACAG
|-
| 86||GGGACAAC||C1-TN5-86||CAAGCAGAAGACGGCATACGAGGGACAACGCGTCAGATGTGTATAAGAGACAG
|-
| 87||ATATTCCC||C1-TN5-87||CAAGCAGAAGACGGCATACGAATATTCCCGCGTCAGATGTGTATAAGAGACAG
|-
| 88||TGTTAAGC||C1-TN5-88||CAAGCAGAAGACGGCATACGATGTTAAGCGCGTCAGATGTGTATAAGAGACAG
|-
| 89||TACGCCTC||C1-TN5-89||CAAGCAGAAGACGGCATACGATACGCCTCGCGTCAGATGTGTATAAGAGACAG
|-
| 90||CACTTATC||C1-TN5-90||CAAGCAGAAGACGGCATACGACACTTATCGCGTCAGATGTGTATAAGAGACAG
|-
| 91||ACCGCTAA||C1-TN5-91||CAAGCAGAAGACGGCATACGAACCGCTAAGCGTCAGATGTGTATAAGAGACAG
|-
| 92||TAAGGTCC||C1-TN5-92||CAAGCAGAAGACGGCATACGATAAGGTCCGCGTCAGATGTGTATAAGAGACAG
|-
| 93||GAAAGGTG||C1-TN5-93||CAAGCAGAAGACGGCATACGAGAAAGGTGGCGTCAGATGTGTATAAGAGACAG
|-
| 94||ACGTTGTA||C1-TN5-94||CAAGCAGAAGACGGCATACGAACGTTGTAGCGTCAGATGTGTATAAGAGACAG
|-
| 95||GCAGAGAA||C1-TN5-95||CAAGCAGAAGACGGCATACGAGCAGAGAAGCGTCAGATGTGTATAAGAGACAG
|-
|-
| CP-2-SeqRead2 ||5\'-CGGTCTGCCATCCGACGGTAGTGT-3\'||24
| 96||GCATTTGG||C1-TN5-96||CAAGCAGAAGACGGCATACGAGCATTTGGGCGTCAGATGTGTATAAGAGACAG
|}
|}

Latest revision as of 17:01, 27 May 2015

Indexes for Library Submission[edit]

[1]

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[edit]

  • 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 more than 4 bases similarity with ours:
Barcode ID Barcode Related sequences Related sequences ID
TruSeq_Ind_1 CGTGAT CGTGAT Ind1
TruSeq_Ind_2 ACATCG ACATCG Ind2
TruSeq_Ind_3 GCCTAA
TruSeq_Ind_4 TGGTCA TGGTCA Ind4
TruSeq_Ind_5 CACTGT CACTGT Ind5
TruSeq_Ind_6 ATTGGC ATTGGC Ind6
TruSeq_Ind_7 GATCTG GATCTG Ind7
TruSeq_Ind_8 TCAAGT TCAAGT Ind8
TruSeq_Ind_9 CTGATC
TruSeq_Ind_10 AAGCTA AAGCTA Ind10
TruSeq_Ind_11 GTAGCC GTAGCC Ind11
TruSeq_Ind_12 TACAAG TACAAG Ind12
TruSeq_Ind_13 TTGACT
TruSeq_Ind_14 GGAACT TGAACT,GGCACT,GGATCT,GGAACG Ind18,Ind43,Ind202,Ind294
TruSeq_Ind_15 TGACAT TGCCAT Ind271
TruSeq_Ind_16 GGACGG GGACGT Ind54
TruSeq_Ind_18 GCGGAC TCGGAC,GCGGAA Ind376,Ind284
TruSeq_Ind_19 TTTCAC ATTCAC,TCTCAC,TTGCAC,TTTCTC Ind353,Ind143,Ind150,Ind156
TruSeq_Ind_20 GGCCAC GGCGAC,GACCAC Ind72,Ind83
TruSeq_Ind_21 CGAAAC GGAAAC,CGAGAC,CCAAAC,CGAAGC Ind193,Ind253,Ind289,Ind293
TruSeq_Ind_22 CGTACG
TruSeq_Ind_23 CCACTC CGACTC,CCAGTC Ind3,Ind263
TruSeq_Ind_25 ATCAGT ATCTGT Ind60
TruSeq_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 for Dual-Index[edit]

  • Sequencing primers: ALL CUSTOM PRIMERS (except i5 read primer is the same as standard)
    • PE Read 1 Sequencing Primer: 5' TGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC (Tm = 79.93 C)
    • PE Read 2 Sequencing Primer: 5' AGGAGTTCGGCTAGGAACGATGAGCCTCCAAC (Tm = 79.15 C)
    • Multiplexing Read 1 Sequencing Primer (i7): 5' GTTGGAGGCTCATCGTTCCTAGCCGAACTCCT (Tm = 79.15 C)
    • Multiplexing Read 2 Sequencing Primer (i5): 5' AATGATACGGCGACCACCGAGATCTACAC (Tm = 74.60 C)
Name Nick-name Barcode Barcode sequence sample sheet Sequence (5\'->3\') Length
AmpF7.S502 S502 CTCTCTAT CTCTCTAT AATGATACGGCGACCACCGAGATCTACACCTCTCTATTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S503 S503 TATCCTCT TATCCTCT AATGATACGGCGACCACCGAGATCTACACTATCCTCTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S505 S505 GTAAGGAG GTAAGGAG AATGATACGGCGACCACCGAGATCTACACGTAAGGAGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S506 S506 ACTGCATA ACTGCATA AATGATACGGCGACCACCGAGATCTACACACTGCATATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S507 S507 AAGGAGTA AAGGAGTA AATGATACGGCGACCACCGAGATCTACACAAGGAGTATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S508 S508 CTAAGCCT CTAAGCCT AATGATACGGCGACCACCGAGATCTACACCTAAGCCTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S510 S510 CGTCTAAT CGTCTAAT AATGATACGGCGACCACCGAGATCTACACCGTCTAATTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S511 S511 TCTCTCCG TCTCTCCG AATGATACGGCGACCACCGAGATCTACACTCTCTCCGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S513 S513 TCGACTAG TCGACTAG AATGATACGGCGACCACCGAGATCTACACTCGACTAGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S515 S515 TTCTAGCT TTCTAGCT AATGATACGGCGACCACCGAGATCTACACTTCTAGCTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S516 S516 CCTAGAGT CCTAGAGT AATGATACGGCGACCACCGAGATCTACACCCTAGAGTTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S517 S517 GCGTAAGA GCGTAAGA AATGATACGGCGACCACCGAGATCTACACGCGTAAGATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S518 S518 CTATTAAG CTATTAAG AATGATACGGCGACCACCGAGATCTACACCTATTAAGTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S520 S520 AAGGCTAT AAGGCTAT AATGATACGGCGACCACCGAGATCTACACAAGGCTATTGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S521 S521 GAGCCTTA GAGCCTTA AATGATACGGCGACCACCGAGATCTACACGAGCCTTATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
AmpF7.S522 S522 TTATGCGA TTATGCGA AATGATACGGCGACCACCGAGATCTACACTTATGCGATGCGGTCAACACTCTCAGATGTTATCGAGGTCCGAC 73
Name Nick-name Barcode Barcode sequence sample sheet Sequence (5\'->3\') Length
AmpR7.N701 N701 TCGCCTTA TAAGGCGA CAAGCAGAAGACGGCATACGAGATTCGCCTTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N702 N702 CTAGTACG CGTACTAG CAAGCAGAAGACGGCATACGAGATCTAGTACGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N703 N703 TTCTGCCT AGGCAGAA CAAGCAGAAGACGGCATACGAGATTTCTGCCTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N704 N704 GCTCAGGA TCCTGAGC CAAGCAGAAGACGGCATACGAGATGCTCAGGAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N705 N705 AGGAGTCC GGACTCCT CAAGCAGAAGACGGCATACGAGATAGGAGTCCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N706 N706 CATGCCTA TAGGCATG CAAGCAGAAGACGGCATACGAGATCATGCCTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N707 N707 GTAGAGAG CTCTCTAC CAAGCAGAAGACGGCATACGAGATGTAGAGAGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N710 N710 CAGCCTCG CGAGGCTG CAAGCAGAAGACGGCATACGAGATCAGCCTCGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N711 N711 TGCCTCTT AAGAGGCA CAAGCAGAAGACGGCATACGAGATTGCCTCTTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N712 N712 TCCTCTAC GTAGAGGA CAAGCAGAAGACGGCATACGAGATTCCTCTACAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N714 N714 TCATGAGC GCTCATGA CAAGCAGAAGACGGCATACGAGATTCATGAGCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N715 N715 CCTGAGAT ATCTCAGG CAAGCAGAAGACGGCATACGAGATCCTGAGATAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N716 N716 TAGCGAGT ACTCGCTA CAAGCAGAAGACGGCATACGAGATTAGCGAGTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N718 N718 GTAGCTCC GGAGCTAC CAAGCAGAAGACGGCATACGAGATGTAGCTCCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N719 N719 TACTACGC GCGTAGTA CAAGCAGAAGACGGCATACGAGATTACTACGCAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N720 N720 AGGCTCCG CGGAGCCT CAAGCAGAAGACGGCATACGAGATAGGCTCCGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N721 N721 GCAGCGTA TACGCTGC CAAGCAGAAGACGGCATACGAGATGCAGCGTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N722 N722 CTGCGCAT ATGCGCAG CAAGCAGAAGACGGCATACGAGATCTGCGCATAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N723 N723 GAGCGCTA TAGCGCTC CAAGCAGAAGACGGCATACGAGATGAGCGCTAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N724 N724 CGCTCAGT ACTGAGCG CAAGCAGAAGACGGCATACGAGATCGCTCAGTAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N726 N726 GTCTTAGG CCTAAGAC CAAGCAGAAGACGGCATACGAGATGTCTTAGGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N727 N727 ACTGATCG CGATCAGT CAAGCAGAAGACGGCATACGAGATACTGATCGAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N728 N728 TAGCTGCA TGCAGCTA CAAGCAGAAGACGGCATACGAGATTAGCTGCAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64
AmpR7.N729 N729 GACGTCGA TCGACGTC CAAGCAGAAGACGGCATACGAGATGACGTCGAAGGAGTTCGGCTAGGAACGATGAGCCTCCAAC 64

Library Free Multiplexing Primers[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

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[edit]

STRT-SEQ Read 1 v3

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

totoRNAseq Read 1: [2]

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)[edit]

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[edit]

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

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

Barcoded adaptors

Name in Illumina TrueSeq kit Sequences (5'-->3')
TruSeq Universal Adapter 5'- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -3'
TruSeq Adapter, Index XX 5'- GATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -3'
  • Note:
    • TruSeq adaptor barcode Index 1-12 are the same as Zhanglab's Index 1-96, but Index13-27 are different as list below.
    • Index numbers 17, 24, and 26 are reserved by Illumina.
Index Barcodes
TruSeq_Ind13 AGTCAA
TruSeq_Ind14 AGTTCC
TruSeq_Ind15 ATGTCA
TruSeq_Ind16 CCGTCC
TruSeq_Ind18 GTCCGC
TruSeq_Ind19 GTGAAA
TruSeq_Ind20 GTGGCC
TruSeq_Ind21 GTTTCG
TruSeq_Ind22 CGTACG
TruSeq_Ind23 GAGTGG
TruSeq_Ind25 ACTGAT
TruSeq_Ind27 ATTCCT

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

Sten's EZ-Tn5 protocol related primers[edit]

C1-P1-PCR-2	/5Biosg/GAATGATACGGCGACCACCGAT
C1-TN5-U	/5Phos/CTGTCTCTTATACACATCTGACGC
Order Barcode Name Sequence
1 CGTCTAAT C1-TN5-1 CAAGCAGAAGACGGCATACGACGTCTAATGCGTCAGATGTGTATAAGAGACAG
2 AGACTCGT C1-TN5-2 CAAGCAGAAGACGGCATACGAAGACTCGTGCGTCAGATGTGTATAAGAGACAG
3 GCACGTCA C1-TN5-3 CAAGCAGAAGACGGCATACGAGCACGTCAGCGTCAGATGTGTATAAGAGACAG
4 TCAACGAC C1-TN5-4 CAAGCAGAAGACGGCATACGATCAACGACGCGTCAGATGTGTATAAGAGACAG
5 ATTTAGCG C1-TN5-5 CAAGCAGAAGACGGCATACGAATTTAGCGGCGTCAGATGTGTATAAGAGACAG
6 ATACAGAC C1-TN5-6 CAAGCAGAAGACGGCATACGAATACAGACGCGTCAGATGTGTATAAGAGACAG
7 TGCGTAGG C1-TN5-7 CAAGCAGAAGACGGCATACGATGCGTAGGGCGTCAGATGTGTATAAGAGACAG
8 TGGAGCTC C1-TN5-8 CAAGCAGAAGACGGCATACGATGGAGCTCGCGTCAGATGTGTATAAGAGACAG
9 TGAATACC C1-TN5-9 CAAGCAGAAGACGGCATACGATGAATACCGCGTCAGATGTGTATAAGAGACAG
10 TCTCACAC C1-TN5-10 CAAGCAGAAGACGGCATACGATCTCACACGCGTCAGATGTGTATAAGAGACAG
11 TACTGGTA C1-TN5-11 CAAGCAGAAGACGGCATACGATACTGGTAGCGTCAGATGTGTATAAGAGACAG
12 ACGATAGG C1-TN5-12 CAAGCAGAAGACGGCATACGAACGATAGGGCGTCAGATGTGTATAAGAGACAG
13 GATGTCGA C1-TN5-13 CAAGCAGAAGACGGCATACGAGATGTCGAGCGTCAGATGTGTATAAGAGACAG
14 TTACGGGT C1-TN5-14 CAAGCAGAAGACGGCATACGATTACGGGTGCGTCAGATGTGTATAAGAGACAG
15 CACAGCAT C1-TN5-15 CAAGCAGAAGACGGCATACGACACAGCATGCGTCAGATGTGTATAAGAGACAG
16 CTTTGACA C1-TN5-16 CAAGCAGAAGACGGCATACGACTTTGACAGCGTCAGATGTGTATAAGAGACAG
17 CCTTCAAG C1-TN5-17 CAAGCAGAAGACGGCATACGACCTTCAAGGCGTCAGATGTGTATAAGAGACAG
18 GAGTCCTG C1-TN5-18 CAAGCAGAAGACGGCATACGAGAGTCCTGGCGTCAGATGTGTATAAGAGACAG
19 CACACTGA C1-TN5-19 CAAGCAGAAGACGGCATACGACACACTGAGCGTCAGATGTGTATAAGAGACAG
20 GTTACAGG C1-TN5-20 CAAGCAGAAGACGGCATACGAGTTACAGGGCGTCAGATGTGTATAAGAGACAG
21 GGACCTTT C1-TN5-21 CAAGCAGAAGACGGCATACGAGGACCTTTGCGTCAGATGTGTATAAGAGACAG
22 TTCCGTTC C1-TN5-22 CAAGCAGAAGACGGCATACGATTCCGTTCGCGTCAGATGTGTATAAGAGACAG
23 ACTGTTTG C1-TN5-23 CAAGCAGAAGACGGCATACGAACTGTTTGGCGTCAGATGTGTATAAGAGACAG
24 AAGTGGCT C1-TN5-24 CAAGCAGAAGACGGCATACGAAAGTGGCTGCGTCAGATGTGTATAAGAGACAG
25 CTGTACAA C1-TN5-25 CAAGCAGAAGACGGCATACGACTGTACAAGCGTCAGATGTGTATAAGAGACAG
26 CGCAAAGT C1-TN5-26 CAAGCAGAAGACGGCATACGACGCAAAGTGCGTCAGATGTGTATAAGAGACAG
27 GTGCATGA C1-TN5-27 CAAGCAGAAGACGGCATACGAGTGCATGAGCGTCAGATGTGTATAAGAGACAG
28 GTCATTAG C1-TN5-28 CAAGCAGAAGACGGCATACGAGTCATTAGGCGTCAGATGTGTATAAGAGACAG
29 AGCTCCTT C1-TN5-29 CAAGCAGAAGACGGCATACGAAGCTCCTTGCGTCAGATGTGTATAAGAGACAG
30 TCACCCGA C1-TN5-30 CAAGCAGAAGACGGCATACGATCACCCGAGCGTCAGATGTGTATAAGAGACAG
31 GTTGCCAC C1-TN5-31 CAAGCAGAAGACGGCATACGAGTTGCCACGCGTCAGATGTGTATAAGAGACAG
32 TGTACCAA C1-TN5-32 CAAGCAGAAGACGGCATACGATGTACCAAGCGTCAGATGTGTATAAGAGACAG
33 AACGAGGT C1-TN5-33 CAAGCAGAAGACGGCATACGAAACGAGGTGCGTCAGATGTGTATAAGAGACAG
34 AGCCACCA C1-TN5-34 CAAGCAGAAGACGGCATACGAAGCCACCAGCGTCAGATGTGTATAAGAGACAG
35 GGTAATCA C1-TN5-35 CAAGCAGAAGACGGCATACGAGGTAATCAGCGTCAGATGTGTATAAGAGACAG
36 CCAGTCCA C1-TN5-36 CAAGCAGAAGACGGCATACGACCAGTCCAGCGTCAGATGTGTATAAGAGACAG
37 ACCTCAGC C1-TN5-37 CAAGCAGAAGACGGCATACGAACCTCAGCGCGTCAGATGTGTATAAGAGACAG
38 GGTGGACT C1-TN5-38 CAAGCAGAAGACGGCATACGAGGTGGACTGCGTCAGATGTGTATAAGAGACAG
39 GACAAACC C1-TN5-39 CAAGCAGAAGACGGCATACGAGACAAACCGCGTCAGATGTGTATAAGAGACAG
40 TAACTCCG C1-TN5-40 CAAGCAGAAGACGGCATACGATAACTCCGGCGTCAGATGTGTATAAGAGACAG
41 ACACCGTG C1-TN5-41 CAAGCAGAAGACGGCATACGAACACCGTGGCGTCAGATGTGTATAAGAGACAG
42 GTAGAACG C1-TN5-42 CAAGCAGAAGACGGCATACGAGTAGAACGGCGTCAGATGTGTATAAGAGACAG
43 GGATTGAC C1-TN5-43 CAAGCAGAAGACGGCATACGAGGATTGACGCGTCAGATGTGTATAAGAGACAG
44 ACGTATCC C1-TN5-44 CAAGCAGAAGACGGCATACGAACGTATCCGCGTCAGATGTGTATAAGAGACAG
45 TTCGGAAA C1-TN5-45 CAAGCAGAAGACGGCATACGATTCGGAAAGCGTCAGATGTGTATAAGAGACAG
46 AGTTGTGT C1-TN5-46 CAAGCAGAAGACGGCATACGAAGTTGTGTGCGTCAGATGTGTATAAGAGACAG
47 AAGCACAT C1-TN5-47 CAAGCAGAAGACGGCATACGAAAGCACATGCGTCAGATGTGTATAAGAGACAG
48 CTGTCATT C1-TN5-48 CAAGCAGAAGACGGCATACGACTGTCATTGCGTCAGATGTGTATAAGAGACAG
49 GTCCTATA C1-TN5-49 CAAGCAGAAGACGGCATACGAGTCCTATAGCGTCAGATGTGTATAAGAGACAG
50 CTACGCTG C1-TN5-50 CAAGCAGAAGACGGCATACGACTACGCTGGCGTCAGATGTGTATAAGAGACAG
51 GGGATTGT C1-TN5-51 CAAGCAGAAGACGGCATACGAGGGATTGTGCGTCAGATGTGTATAAGAGACAG
52 TGATGTAG C1-TN5-52 CAAGCAGAAGACGGCATACGATGATGTAGGCGTCAGATGTGTATAAGAGACAG
53 TTCGCTGT C1-TN5-53 CAAGCAGAAGACGGCATACGATTCGCTGTGCGTCAGATGTGTATAAGAGACAG
54 GAAGACTT C1-TN5-54 CAAGCAGAAGACGGCATACGAGAAGACTTGCGTCAGATGTGTATAAGAGACAG
55 TCTGGGCA C1-TN5-55 CAAGCAGAAGACGGCATACGATCTGGGCAGCGTCAGATGTGTATAAGAGACAG
56 CAACTAGA C1-TN5-56 CAAGCAGAAGACGGCATACGACAACTAGAGCGTCAGATGTGTATAAGAGACAG
57 CCATGGGA C1-TN5-57 CAAGCAGAAGACGGCATACGACCATGGGAGCGTCAGATGTGTATAAGAGACAG
58 ATGCGACG C1-TN5-58 CAAGCAGAAGACGGCATACGAATGCGACGGCGTCAGATGTGTATAAGAGACAG
59 GAGGGTAG C1-TN5-59 CAAGCAGAAGACGGCATACGAGAGGGTAGGCGTCAGATGTGTATAAGAGACAG
60 CGGGTGAA C1-TN5-60 CAAGCAGAAGACGGCATACGACGGGTGAAGCGTCAGATGTGTATAAGAGACAG
61 GCCATCTT C1-TN5-61 CAAGCAGAAGACGGCATACGAGCCATCTTGCGTCAGATGTGTATAAGAGACAG
62 GCATAATC C1-TN5-62 CAAGCAGAAGACGGCATACGAGCATAATCGCGTCAGATGTGTATAAGAGACAG
63 TCTATGGT C1-TN5-63 CAAGCAGAAGACGGCATACGATCTATGGTGCGTCAGATGTGTATAAGAGACAG
64 AGGACTTA C1-TN5-64 CAAGCAGAAGACGGCATACGAAGGACTTAGCGTCAGATGTGTATAAGAGACAG
65 CGTGATTC C1-TN5-65 CAAGCAGAAGACGGCATACGACGTGATTCGCGTCAGATGTGTATAAGAGACAG
66 ACTAGCGA C1-TN5-66 CAAGCAGAAGACGGCATACGAACTAGCGAGCGTCAGATGTGTATAAGAGACAG
67 GTAACTCC C1-TN5-67 CAAGCAGAAGACGGCATACGAGTAACTCCGCGTCAGATGTGTATAAGAGACAG
68 CGGAAGTG C1-TN5-68 CAAGCAGAAGACGGCATACGACGGAAGTGGCGTCAGATGTGTATAAGAGACAG
69 CCGAGTAC C1-TN5-69 CAAGCAGAAGACGGCATACGACCGAGTACGCGTCAGATGTGTATAAGAGACAG
70 GACGCAAT C1-TN5-70 CAAGCAGAAGACGGCATACGAGACGCAATGCGTCAGATGTGTATAAGAGACAG
71 ACCTGGAG C1-TN5-71 CAAGCAGAAGACGGCATACGAACCTGGAGGCGTCAGATGTGTATAAGAGACAG
72 CATGGGTT C1-TN5-72 CAAGCAGAAGACGGCATACGACATGGGTTGCGTCAGATGTGTATAAGAGACAG
73 ATTCCTAG C1-TN5-73 CAAGCAGAAGACGGCATACGAATTCCTAGGCGTCAGATGTGTATAAGAGACAG
74 AATCATGC C1-TN5-74 CAAGCAGAAGACGGCATACGAAATCATGCGCGTCAGATGTGTATAAGAGACAG
75 GCTTCCCT C1-TN5-75 CAAGCAGAAGACGGCATACGAGCTTCCCTGCGTCAGATGTGTATAAGAGACAG
76 AGGTAAAG C1-TN5-76 CAAGCAGAAGACGGCATACGAAGGTAAAGGCGTCAGATGTGTATAAGAGACAG
77 CCACAACT C1-TN5-77 CAAGCAGAAGACGGCATACGACCACAACTGCGTCAGATGTGTATAAGAGACAG
78 ACAGGCAT C1-TN5-78 CAAGCAGAAGACGGCATACGAACAGGCATGCGTCAGATGTGTATAAGAGACAG
79 TTTGTGTC C1-TN5-79 CAAGCAGAAGACGGCATACGATTTGTGTCGCGTCAGATGTGTATAAGAGACAG
80 TGAGCATA C1-TN5-80 CAAGCAGAAGACGGCATACGATGAGCATAGCGTCAGATGTGTATAAGAGACAG
81 TTAGACGC C1-TN5-81 CAAGCAGAAGACGGCATACGATTAGACGCGCGTCAGATGTGTATAAGAGACAG
82 CGCTTGCT C1-TN5-82 CAAGCAGAAGACGGCATACGACGCTTGCTGCGTCAGATGTGTATAAGAGACAG
83 AGTCTGCC C1-TN5-83 CAAGCAGAAGACGGCATACGAAGTCTGCCGCGTCAGATGTGTATAAGAGACAG
84 CATAGTCG C1-TN5-84 CAAGCAGAAGACGGCATACGACATAGTCGGCGTCAGATGTGTATAAGAGACAG
85 TCTTGCTG C1-TN5-85 CAAGCAGAAGACGGCATACGATCTTGCTGGCGTCAGATGTGTATAAGAGACAG
86 GGGACAAC C1-TN5-86 CAAGCAGAAGACGGCATACGAGGGACAACGCGTCAGATGTGTATAAGAGACAG
87 ATATTCCC C1-TN5-87 CAAGCAGAAGACGGCATACGAATATTCCCGCGTCAGATGTGTATAAGAGACAG
88 TGTTAAGC C1-TN5-88 CAAGCAGAAGACGGCATACGATGTTAAGCGCGTCAGATGTGTATAAGAGACAG
89 TACGCCTC C1-TN5-89 CAAGCAGAAGACGGCATACGATACGCCTCGCGTCAGATGTGTATAAGAGACAG
90 CACTTATC C1-TN5-90 CAAGCAGAAGACGGCATACGACACTTATCGCGTCAGATGTGTATAAGAGACAG
91 ACCGCTAA C1-TN5-91 CAAGCAGAAGACGGCATACGAACCGCTAAGCGTCAGATGTGTATAAGAGACAG
92 TAAGGTCC C1-TN5-92 CAAGCAGAAGACGGCATACGATAAGGTCCGCGTCAGATGTGTATAAGAGACAG
93 GAAAGGTG C1-TN5-93 CAAGCAGAAGACGGCATACGAGAAAGGTGGCGTCAGATGTGTATAAGAGACAG
94 ACGTTGTA C1-TN5-94 CAAGCAGAAGACGGCATACGAACGTTGTAGCGTCAGATGTGTATAAGAGACAG
95 GCAGAGAA C1-TN5-95 CAAGCAGAAGACGGCATACGAGCAGAGAAGCGTCAGATGTGTATAAGAGACAG
96 GCATTTGG C1-TN5-96 CAAGCAGAAGACGGCATACGAGCATTTGGGCGTCAGATGTGTATAAGAGACAG