Wednesday, September 24, 2008

Solexa Library Primer Sequences [ZT]

Solexa Library Primer Sequences

Sequences for Solexa Library Preparations:

Oligonucleotide sequences. (C)2006 and 2008 Illumina, Inc. All rights reserved.

Genomic DNA oligonucleotide sequences
Adapters1

5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG

5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT
PCR Primers1

5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT

5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
Genomic DNA Sequencing Primer

5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT


Paired End DNA oligonucleotide sequences
PE Adapters1

5' P-GATCGGAAGAGCGGTTCAGCAGGAATGCCGAG

5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT
PE PCR Primers1

5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT

5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT

PE Sequencing Primer

5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

5' CGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT

DpnII gene expression oligonucleotide sequences
Gex Adapter 1

5' P-GATCGTCGGACTGTAGAACTCTGAAC

5’ ACAGGTTCAGAGTTCTACAGTCCGAC
Gex Adapter 2

5' CAAGCAGAAGACGGCATACGANN

5' P-TCGTATGCCGTCTTCTGCTTG
Gex PCR Primer 1

5' CAAGCAGAAGACGGCATACGA
Gex PCR Primer 2

5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
Gex Sequencing Primer

5' CGACAGGTTCAGAGTTCTACAGTCCGACGATC


NlaIII gene expression oligonucleotide sequences
Gex Adapter 1

5' P-TCGGACTGTAGAACTCTGAAC

5' ACAGGTTCAGAGTTCTACAGTCCGACATG
Gex Adapter 2

5' CAAGCAGAAGACGGCATACGANN

5' P-TCGTATGCCGTCTTCTGCTTG
Gex PCR Primer 1

5' CAAGCAGAAGACGGCATACGA

Gex PCR Primer 2

5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA

Gex Sequencing Primer

5' CCGACAGGTTCAGAGTTCTACAGTCCGACATG


Small RNA oligonucleotide sequences
RT Primer

5' CAAGCAGAAGACGGCATACGA
5' RNA Adapter

5' GUUCAGAGUUCUACAGUCCGACGAUC
3' RNA Adapter

5' P-UCGUAUGCCGUCUUCUGCUUGUidT
Small RNA PCR Primer 1

5' CAAGCAGAAGACGGCATACGA
Small RNA PCR Primer 2

5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
Small RNA Sequencing Primer

5' CGACAGGTTCAGAGTTCTACAGTCCGACGATC


Re-arrange those sequences:

Genomic DNA

Adapter:
5' -------------------- -----ACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (-) -------------------- -------------- 3'
3' -------------------- -----TGTGAGAAAGGGATG TGCTGCGAGAAGGCTAGp (-) -------------------- -------------- 5'
Adapter:
5' -------------------- -------------------- ------------------ (-) pGATCGGAAGAGCTCGTATG CCGTCTTCTGCTTG 3'
3' -------------------- -------------------- ------------------ (-) TCTAGCCTTCTCGAGCATAC GGCAGAAGACGAAC 5'
PCR Primer:
5' AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (-) -------------------- -------------- 3'
3' -------------------- -------------------- ------------------ (-) -------------------- -------------- 5'
PCR Primer:
5' -------------------- -------------------- ------------------ (-) -------------------- -------------- 3'
3' -------------------- -------------------- ------------------ (-) TCTAGCCTTCTCGAGCATAC GGCAGAAGACGAAC 5'
Result Library:
5' AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (N) AGATCGGAAGAGCTCGTATG CCGTCTTCTGCTTG 3'
3' TTACTATGCCGCTGGTGGCT CTAGATGTGAGAAAGGGATG TGCTGCGAGAAGGCTAGA (N) TCTAGCCTTCTCGAGCATAC GGCAGAAGACGAAC 5'
Genomic DNA Sequencing Primer:
5' -------------------- -----ACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (-) -------------------- -------------- 3'
3' -------------------- -------------------- ------------------ (-) -------------------- -------------- 5'

DpnII gene expression

Gex Adapter 1:
5' -------------------A CAGGTTCAGAGTTCTACAGT CCGAC--------------- -------------------- ------ 3'
3' -------------------- ---CAAGTCTCAAGATGTCA GGCTGCTAGp---------- -------------------- ------ 5'
Gex Adapter 2:
5' -------------------- -------------------- -------------------- ----pTCGTATGCCGTCTTC TGCTTG 3'
3' -------------------- -------------------- -------------------- ---NNAGCATACGGCAGAAG ACGAAC 5'
Gex PCR Primer 1:
5' -------------------- -------------------- ----------------------------------------- ------ 3'
3' -------------------- -------------------- -------------------- -----AGCATACGGCAGAAG ACGAAC 5'
Gex PCR Primer 2:
5' AATGATACGGCGACCACCGA CAGGTTCAGAGTTCTACAGT CCGA---------------- -------------------- ------ 3'
3' -------------------- -------------------- -------------------- -------------------- ------ 5'
Result Library:
5' AATGATACGGCGACCACCGA CAGGTTCAGAGTTCTACAGT CCGACGATCNNNNNNNNNNN NNNNNTCGTATGCCGTCTTC TGCTTG 3'
3' TTACTATGCCGCTGGTGGCT GTCCAAGTCTCAAGATGTCA GGCTGCTAGNNNNNNNNNNN NNNNNAGCATACGGCAGAAG ACGAAC 5'
Gex Sequencing Primer:
5' -----------------CGA CAGGTTCAGAGTTCTACAGT CCGACGATC----------- -------------------- ------ 3'
3'--------------------- -------------------- -------------------- -------------------- ------ 5'

NlaIII gene expression

Gex Adapter 1:
5' -------------------A CAGGTTCAGAGTTCTACAGT CCGACATG------------ -------------------- ------ 3'
3' -------------------- ---CAAGTCTCAAGATGTCA GGCTp--------------- -------------------- ------ 5'
Gex Adapter 2:
5' -------------------- -------------------- -------------------- ----pTCGTATGCCGTCTTC TGCTTG 3'
3' -------------------- -------------------- -------------------- ---NNAGCATACGGCAGAAG ACGAAC 5'
Gex PCR Primer 1:
5' -------------------- -------------------- -------------------- -------------------- ------ 3'
3' -------------------- -------------------- -------------------- -----AGCATACGGCAGAAG ACGAAC 5'
Gex PCR Primer 2:
5' AATGATACGGCGACCACCGA CAGGTTCAGAGTTCTACAGT CCGA---------------- -------------------- ------ 3'
3' -------------------- -------------------- -------------------- -------------------- ------ 5'
Result Library:
5' AATGATACGGCGACCACCGA CAGGTTCAGAGTTCTACAGT CCGACATGNNNNNNNNNNNN NNNNNTCGTATGCCGTCTTC TGCTTG 3'
3' TTACTATGCCGCTGGTGGCT GTCCAAGTCTCAAGATGTCA GGCTGTACNNNNNNNNNNNN NNNNNAGCATACGGCAGAAG ACGAAC 5'
Gex Sequencing Primer:
5' ----------------CCGA CAGGTTCAGAGTTCTACAGT CCGACATG------------ -------------------- ------ 3'
3' -------------------- -------------------- -------------------- -------------------- ------ 5'

Small RNA

5' RNA Adapter:
5' -------------------- ---GUUCAGAGUUCUACAGU CCGACGAUC (-) -------------------- - 3'
3' -------------------- -------------------- --------- (-) -------------------- - 5'
3' RNA Adapter:
5' -------------------- -------------------- --------- (-)pUCGUAUGCCGUCUUCUGCUU GUidT 3'
3' -------------------- -------------------- --------- (-) -------------------- - 5'
RT Primer:
5' -------------------- -------------------- --------- (-) -------------------- - 3'
3' -------------------- -------------------- --------- (-) AGCATACGGCAGAAGACGAA C 5'
Small RNA PCR Primer 1:
5' -------------------- -------------------- --------- (-) -------------------- - 3'
3' -------------------- -------------------- --------- (-) AGCATACGGCAGAAGACGAA C 5'

Small RNA PCR Primer 2:
5' AATGATACGGCGACCACCGA CAGGTTCAGAGTTCTACAGT CCGA----- (-) -------------------- - 3'
3' -------------------- -------------------- --------- (-) -------------------- - 5'

Result Library:
5' AATGATACGGCGACCACCGA CAGGTTCAGAGTTCTACAGT CCGACGATC (N) TCGTATGCCGTCTTCTGCTT G 3'
3' TTACTATGCCGCTGGTGGCT GTCCAAGTCTCAAGATGTCA GGCTGCTAG (N) AGCATACGGCAGAAGACGAA C 5'
Small RNA Sequencing Primer:
5' -----------------CGA CAGGTTCAGAGTTCTACAGT CCGACGATC (-) -------------------- - 3'
3' -------------------- -------------------- --------- (-) -------------------- - 5'


Paired-end DNA

PE Adapter1:
5' -------------------- -----ACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (-) -------------------- -------------------- -------------------- - 3'
3' -------------------- -----TGTGAGAAAGGGATG TGCTGCGAGAAGGCTAGp (-) -------------------- -------------------- -------------------- - 5'
PE Adapter2:
5' -------------------- -------------------- ------------------ (-) pGATCGGAAGAGCGGTTCAG CAGGAATGCCGAG------- -------------------- - 3'
3' -------------------- -------------------- ------------------ (-) TCTAGCCTTCTCGCCAAGTC GTCCTTACGGCTC------- -------------------- - 5'
PE PCR Primer1:
5' AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (-) -------------------- -------------------- -------------------- - 3'
3' -------------------- -------------------- ------------------ (-) -------------------- -------------------- -------------------- - 5'
PE PCR Primer2:
5' -------------------- -------------------- ------------------ (-) -------------------- -------------------- -------------------- - 3'
3' -------------------- -------------------- ------------------ (-) TCTAGCCTTCTCGCCAAGTC GTCCTTACGGCTCTGGCTAG AGCATACGGCAGAAGACGAA C 5'

Result Library:
5' AATGATACGGCGACCACCGA GATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (N) AGATCGGAAGAGCGGTTCAG CAGGAATGCCGAGACCGATC TCGTATGCCGTCTTCTGCTT G 3'
3' TTACTATGCCGCTGGTGGCT CTAGATGTGAGAAAGGGATG TGCTGCGAGAAGGCTAGA (N) TCTAGCCTTCTCGCCAAGTC GTCCTTACGGCTCTGGCTAG AGCATACGGCAGAAGACGAA C 5'

PE DNA Sequencing Primer1
5' -------------------- -----ACACTCTTTCCCTAC ACGACGCTCTTCCGATCT (-) -------------------- -------------------- -------------------- - 3'
3' -------------------- -------------------- ------------------ (-) -------------------- -------------------- -------------------- - 5'
PE DNA Sequencing Primer2
5' -------------------- -------------------- ------------------ (-) -------------------- -------------------- -------------------- - 3'
3' -------------------- -------------------- ------------------ (-) TCTAGCCTTCTCGCCAAGTC GTCCTTACGGCTCTGGC--- -------------------- - 5'


1 comment:

shenrk said...

I copied those information from SeqAnswers.com