Difference between revisions of "Template:Groningen/Primers"

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    <h5>Synthetic DNA fragments</h5>
 
     <table><tr><th>Synthetic DNA sequences</th><th>Source</th></tr><tr><td>ss1-V5-EGII-DocS</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>ss1-FLAG-CBHI-DocS</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>ss1-myc-BGLI-DocA part1</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>ss1-myc-BGLI-DocA part2</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>AGA2-CIPA3-His part1</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>AGA2-CIPA3-His part2</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>synthetic PAL2 gene part1</td><td>"Ordered from IDTA, designed based on McKenna, 2014"</td></tr><tr><td>synthetic PAL2 gene part2</td><td>"Ordered from IDTA, designed based on McKenna, 2014"</td></tr></table>
 
     <table><tr><th>Synthetic DNA sequences</th><th>Source</th></tr><tr><td>ss1-V5-EGII-DocS</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>ss1-FLAG-CBHI-DocS</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>ss1-myc-BGLI-DocA part1</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>ss1-myc-BGLI-DocA part2</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>AGA2-CIPA3-His part1</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>AGA2-CIPA3-His part2</td><td>"Ordered from IDTA, designed based on Wen et al. 2010"</td></tr><tr><td>synthetic PAL2 gene part1</td><td>"Ordered from IDTA, designed based on McKenna, 2014"</td></tr><tr><td>synthetic PAL2 gene part2</td><td>"Ordered from IDTA, designed based on McKenna, 2014"</td></tr></table>
  
 
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<h5><i>Saccharomyces cerevisiae</i> strains</h5>
 
     <table><tr><th>Strains</th><th>Source</th></tr><tr><td>BJ1991</td><td>"Molecular Cell Biology group, RUG"</td></tr><tr><td>BY4741</td><td>"Molmic group, RUG"</td></tr><tr><td>BJC3CB</td><td>This work</td></tr><tr><td>BJC1CB</td><td>This work</td></tr><tr><td>YPH499</td><td>"Molecular Cell Biology group, RUG"</td></tr><tr><td>YPHPAL2</td><td>This work</td></tr><tr><td>YPHCON</td><td>This work</td></tr></table>
 
     <table><tr><th>Strains</th><th>Source</th></tr><tr><td>BJ1991</td><td>"Molecular Cell Biology group, RUG"</td></tr><tr><td>BY4741</td><td>"Molmic group, RUG"</td></tr><tr><td>BJC3CB</td><td>This work</td></tr><tr><td>BJC1CB</td><td>This work</td></tr><tr><td>YPH499</td><td>"Molecular Cell Biology group, RUG"</td></tr><tr><td>YPHPAL2</td><td>This work</td></tr><tr><td>YPHCON</td><td>This work</td></tr></table>
  
 
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<br>
 
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 +
<h5>Plasmids</h5>
 
     <table><tr><th>Plasmids</th><th>Source</th></tr><tr><td>pYD1-CipA3-EGII</td><td>From Wen et al. 2010</td></tr><tr><td>pYD1-CipA1-EGII</td><td>From Wen et al. 2010</td></tr><tr><td>pRS425-CBHII-BGL1</td><td>From Wen et al. 2010</td></tr><tr><td>p414 KanMX TEF1-Cas9-Tcyc</td><td>"Molmic group, RUG"</td></tr><tr><td>pMEL16 OR1</td><td>"Molmic group, RUG"</td></tr><tr><td>pMEL16-ARO10tar</td><td>This work</td></tr><tr><td>pMEL16-AGA2tar</td><td>This work</td></tr><tr><td>pMEL16-AGA1tar</td><td>This work</td></tr><tr><td>pUC57-PAL2</td><td>"Roelfes group, RUG"</td></tr><tr><td>pRS313+ s promHxt7-MCS-terHxt7</td><td>"Molmic group, RUG"</td></tr><tr><td>pRS313-Hxt7-PAL2</td><td>This work</td></tr></table>
 
     <table><tr><th>Plasmids</th><th>Source</th></tr><tr><td>pYD1-CipA3-EGII</td><td>From Wen et al. 2010</td></tr><tr><td>pYD1-CipA1-EGII</td><td>From Wen et al. 2010</td></tr><tr><td>pRS425-CBHII-BGL1</td><td>From Wen et al. 2010</td></tr><tr><td>p414 KanMX TEF1-Cas9-Tcyc</td><td>"Molmic group, RUG"</td></tr><tr><td>pMEL16 OR1</td><td>"Molmic group, RUG"</td></tr><tr><td>pMEL16-ARO10tar</td><td>This work</td></tr><tr><td>pMEL16-AGA2tar</td><td>This work</td></tr><tr><td>pMEL16-AGA1tar</td><td>This work</td></tr><tr><td>pUC57-PAL2</td><td>"Roelfes group, RUG"</td></tr><tr><td>pRS313+ s promHxt7-MCS-terHxt7</td><td>"Molmic group, RUG"</td></tr><tr><td>pRS313-Hxt7-PAL2</td><td>This work</td></tr></table>
  

Revision as of 21:26, 17 October 2018

Primers, plasmids, and strains used during this project


Primers
CRISPR-Cas Primerssequence
588 FWCTTGAAAACTTACGCTCATCTCTTCGACG
589 RVCGGACTTAAGAAAATCCAGGATTGTCTTTCC
6006 FWGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTC
6005 RVGATCATTTATCTTTCACTGCGGAGAAG
F ARO10 tarTGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCAATATACGAACGAAA
CAATGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC
R ARO10 tarGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACCATTGTTTCGTTCGTATA
TTGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA
F AGA2 KO tarTGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCAAAACATACTGTGTGT
TTATGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC
R AGA2 KO tarGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACATAAACACACAGTATGT
TTTGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA
F AGA1 OE tarTGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCTTACGTTCATCTTTGAA
AAAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC
R AGA1 OE tarGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACTTTTTCAAAGATGAACGT
AAGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA
CCasR1-RVCGTGTAATCTGTGACAATTTCGATGCGTACACTGCGGCCCCGAAGTAGCATAGCTTATCTGGATCTG
AACCTCGACTTTCTGGATCAGCC
CCasR2-FWAGATAAGCTATGCTACTTCGGGGCCGCAGTGTACGCATCGAAATTGTCACAGATTACACGCGCTCT
AGCATGGAACCAAGACCCATGACG
CCasR2-RVTGAAATGTTATTATGTACCTCAGTACGCGCTAACATCCCTGGGTTACGCATCACTACATTGGATCTG
AACCTCGACTTTCTGGATCAGCC
CCasR3-RVTGTATCGAGCGATGTACGAATACTCTTGCCGAGTCATAGCAGTGCAGTAGAGCCTGACCCGGATCT
GAACCTCGACTTTCTGGATCAGCC
CCasR3FWAATGTAGTGATGCGTAACCCAGGGATGTTAGCGCGTACTGAGGTACATAATAACATTTCACGCTCT
AGCATGGAACCAAGACCCATGACG
CCasR4-FWGGGTCAGGCTCTACTGCACTGCTATGACTCGGCAAGAGTATTCGTACATCGCTCGATACACGCTCTA
GCATGGAACCAAGACCCATGACG
CCasR5-FWGCTCTCAACAGTCACTTGTGTGCCAAAATATTATACCTACTTCATACATTTTCAATTAAGCGCTCTAG
CATGGAACCAAGACCCATGACG
CCasR5-RVTAATCTTACACTAGTTTATAAGTGTCACGAACGATGAAATGGAAACTTGGGGGGGAAGGCGGATCT
GAACCTCGACTTTCTGGATCAGCC
CCasR1-FWACAAGTTGACGCGACTTCTGTAAAGTTTATTTACAAGATAACAAAGAAACTCCCTTAAGCCGCTCTA
GCATGGAACCAAGACCCATGACG
CCasR4-RVTGTTAATGAACAGAAAACGAACAATTGGTAGCAGTGTTTTATAATTGCGCCCACAAGTTTGGATCTG
AACCTCGACTTTCTGGATCAGCC
CCasAga1-FWGCGCAGAATAATGATCTATCATCAATAATTATCGTGAACTTTTCCAGTATTTACGTTCATGCATGGAA
CCAAGACCCATGA
CCasAga1-RVATTAGTTAATCCCAACAATATTGTGAACAGGTAGGTAAAATGAGCGAAAGATAATGTCATACGAAT
GTACTAATTAAAAGATCAGAAAA

Cellulosome primerssequence
BGLI-fragA-fwTAGTAATGCAGACACTTGCG
BGLI-fragA-rvCAACAGCGGTCTACTGAATC
BGLI-fragB-fwCACTAGCTCAGATTCAGTAGACC
BGLI-fragB-rvCGAGATGGACCGCAAG
BGLI1-FWTTTGGATCCGTCTAGATGAA
BGL1-RVAAACTCGAGTACTAGTATTC
BGL1A-FWTTTGGATCCGTCTAGATGAGATTTCCTTCAATTTTTAC
BGL1A-RVAAACTCGAGTACTAGTACTAATAAGGTAGGTGGGGTA
CBHII1-FWTTTGGATCCGTCTAGATGAA
CBHII1-RVAAACTCGAGTACTAGTAACT
CIPA3A-FWTTTGGATCCGTCTAGATGCA
CIPA3A-RVAAAGTCGACCTCGAGTACTA
CIPA3B-FWTTTGGATCCGTCTAGATGCAGTTACTTCGCTGTTT
CIPA3B-RVAAACTCGAGTACTAGTATTAGTGATGGTGATGGTGATGTTCGAAGGGCCCATTCGAAT
CIPA3C-RVAAAGTCGACCTCGAGTATCA
EGII1-FWTTTGGATCCGTCTAGATGAA
EGII1-RVAAACTCGAGTACTAGTAGAC
Bio-His-EG-FW1TATTTGAATTCGCGGCCGCTTCTAGATGCATCATCACCATCACCATG
Bio-His-EG-RV1TATTTCTGCAGCGGCCGCTACTAGTATTACTTTCTTGCGAGACACGAG
Bio-ss1-HEGII-FW1TATTTGAATTCGCGGCCGCTTCTAGATGAAGGTTTTGATTGTCTTG
Int-ss1-HEGII-FW1TTTGGATCCGTCTAGATGATGAAGGTTTTGATTGTCTTG
Int-ss1-HEGII-RV1AAACTCGAGTACTAGTATTACTTTCTTGCGAGACACGAGC


PAL2 primerssequence
PAL2A-FWTTTGGATCCGTCTAGATGGA
PAL2A-RVAAACTCGAGTACTAGTATTAGCAAATCGGAATCGGAGCTC
PAL2B-FWTTTGGATCCATGCATCACCATCACCATCACGATCAAATCGAAGCAATGTT
PAL2B-RVAAACTCGAGTACTAGTATTAATGGTGATGGTGATGGTGGCAAATCGGAATCGGAGC
PAL2C-FWTTTGGATCCGTCTAGATGGATCAAATCGAAGCAAT
PAL2.1-FWCACTAGCTCAGATTCAGTAG
PAL2.1-RVAAACCATGGATAGCCTTGTT
PAL2.2-RVTTAGCAGATTGGGATTGGGG
PAL2D-FWATATACCAGCATTTAAGAACCTAATGAGTTCTGTTTGTAATGCG
PAL2D-RVAGGTTCTTAAATGCTGGTATATTCGGAAACACGAAGGAGA
Pal2F-fwTTTGGATCCGTCTAGATGGATCAAATAGAAGCAAT
Pal2F-rvAAACTCGAGTTAGTGATGGTGATGGTGATGGCAGATTGGGATTGGGGCAC
Pal2G-fwTTTGGATCCATGCATCACCATCACCATCACATGGATCAAATAGAAGCAAT
Pal2G-rvAAACTCGAGTACTAGTATTAGCAGATTGGGATTGGGG
PAL2-fragA-fwTTTGGATCCGATGGATCAAATAGAAGCAATGTTG
PAL2-fragA-rvAAACCATGGATAGCCTTGTTTC
PAL2-fragB-fwACTAGCTCAGATTCAGTAGACC
PAL2-fragB-rvAAACTCGAGTTAGCAGATTGGGATTGGGG
P T7GACCATCACACCACTGAAGACTGCGG
R T7GTGATCATGAATTAATAAAAGTGTTCGC
PAL2-BB-fix-fwTTAATGAATTCGCGGCCGCTTCTAGATGGACCAAATTGAGGCGATG
PAL2-BB-fix-rvTTAATCTGCAGCGGCCGCTACTAGTACAGTTAGCAAATCGGAATCG
PAL2-BB-fwGAATTCGCGGCCGCTTCTAGATGGACCAAATTGAGGCGATG
PAL2-BB-rvCTGCAGCGGCCGCTACTAGTACAGTTAGCAAATCGGAATCG


Sequencing primerssequence
genseqFWGCAGACGACTCGAATAAG
genseqRVAGCTCGTCAATAGTGGAGATTAC
VR primer fwATTACCGCCTTTGAGTGAGC
VR primer rvTGCCACCTGACGTCTAAGAA
M13 fwGTAAAACGACGGCCAGT
M13 rvCAGGAAACAGCTATGAC
EGII-seq-fwGGCTGTACCACAGATGG
EGII-seq-rvGTTCTGTCGGAGCCAAG
BGL1-seq-paper-FWGCAACAGCCAAGCATTAC
BGL1-seq2-paper-FWACCACAGCGAGGTTATTC
PAL2-seq-ver-RVGTGGTGCTCATCAGTTTC
PAL2-seq-fw-internalCTGCGTGGCACCATTAC

Zeocin cassette primerssequence
Zcas1-FWTATTTGAATTCGCGGCCGCTTCTAGAGTCCAGAAAGTCGAGGTTCAG
Zcas2-FWTATTTGAATTCGCGGCCGCTTCTAGAGGGGCTGATCCAGAAAGTCGA
Zcas3-FWTATTTGAATTCGCGGCCGCTTCTAGAGCCAGAAAGTCGAGGTTCAG
Zcas4-FWTATTTGAATTCGCGGCCGCTTCTAGAGGATCCAGAAAGTCGAGGTTCAG
Zcas1-RVTATTTCTGCAGCGGCCGCTACTAGTATTATGCTTCCGGCTCGTATG
Zcas2-RVTATTTCTGCAGCGGCCGCTACTAGTACTTCCGGCTCGTATGTTGTG
Zcas3-RVTATTTCTGCAGCGGCCGCTACTAGTAGCTCGGAATTAACCCTCAC


Synthetic DNA fragments
Synthetic DNA sequencesSource
ss1-V5-EGII-DocS"Ordered from IDTA, designed based on Wen et al. 2010"
ss1-FLAG-CBHI-DocS"Ordered from IDTA, designed based on Wen et al. 2010"
ss1-myc-BGLI-DocA part1"Ordered from IDTA, designed based on Wen et al. 2010"
ss1-myc-BGLI-DocA part2"Ordered from IDTA, designed based on Wen et al. 2010"
AGA2-CIPA3-His part1"Ordered from IDTA, designed based on Wen et al. 2010"
AGA2-CIPA3-His part2"Ordered from IDTA, designed based on Wen et al. 2010"
synthetic PAL2 gene part1"Ordered from IDTA, designed based on McKenna, 2014"
synthetic PAL2 gene part2"Ordered from IDTA, designed based on McKenna, 2014"


Saccharomyces cerevisiae strains
StrainsSource
BJ1991"Molecular Cell Biology group, RUG"
BY4741"Molmic group, RUG"
BJC3CBThis work
BJC1CBThis work
YPH499"Molecular Cell Biology group, RUG"
YPHPAL2This work
YPHCONThis work


Plasmids
PlasmidsSource
pYD1-CipA3-EGIIFrom Wen et al. 2010
pYD1-CipA1-EGIIFrom Wen et al. 2010
pRS425-CBHII-BGL1From Wen et al. 2010
p414 KanMX TEF1-Cas9-Tcyc"Molmic group, RUG"
pMEL16 OR1"Molmic group, RUG"
pMEL16-ARO10tarThis work
pMEL16-AGA2tarThis work
pMEL16-AGA1tarThis work
pUC57-PAL2"Roelfes group, RUG"
pRS313+ s promHxt7-MCS-terHxt7"Molmic group, RUG"
pRS313-Hxt7-PAL2This work