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== | ||
* | * 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 237: | Line 441: | ||
|}<br> | |}<br> | ||
== Primers 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 259: | Line 464: | ||
|- | |- | ||
| CP-2-IndSeq.x (IndexRead)||5’-ACACTACCGTCGGATGGCAGACCG-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 | |||
|- | |||
| 96||GCATTTGG||C1-TN5-96||CAAGCAGAAGACGGCATACGAGCATTTGGGCGTCAGATGTGTATAAGAGACAG | |||
|} | |} |
Latest revision as of 17:01, 27 May 2015
Indexes for Library Submission[edit]
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
- [1] supp
- [2] Improved protocols for the Illumina GA
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 |
- 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[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 |
- 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[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]
- Reference: [3]
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' |
- -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 ZhangLab_NEBNext_MultiplexingPrimers_BarcodeInfo_06142013
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
[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 |