Difference between revisions of "Template:Groningen/Primers"

Latest revision as of 21:28, 17 October 2018

Primers, plasmids, and strains used during this project

Primers

CRISPR-Cas Primers	sequence
588 FW	CTTGAAAACTTACGCTCATCTCTTCGACG
589 RV	CGGACTTAAGAAAATCCAGGATTGTCTTTCC
6006 FW	GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTC
6005 RV	GATCATTTATCTTTCACTGCGGAGAAG
F ARO10 tar	TGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCAATATACGAACGAAA CAATGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC
R ARO10 tar	GTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACCATTGTTTCGTTCGTATA TTGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA
F AGA2 KO tar	TGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCAAAACATACTGTGTGT TTATGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC
R AGA2 KO tar	GTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACATAAACACACAGTATGT TTTGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA
F AGA1 OE tar	TGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCTTACGTTCATCTTTGAA AAAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC
R AGA1 OE tar	GTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACTTTTTCAAAGATGAACGT AAGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA
CCasR1-RV	CGTGTAATCTGTGACAATTTCGATGCGTACACTGCGGCCCCGAAGTAGCATAGCTTATCTGGATCTG AACCTCGACTTTCTGGATCAGCC
CCasR2-FW	AGATAAGCTATGCTACTTCGGGGCCGCAGTGTACGCATCGAAATTGTCACAGATTACACGCGCTCT AGCATGGAACCAAGACCCATGACG
CCasR2-RV	TGAAATGTTATTATGTACCTCAGTACGCGCTAACATCCCTGGGTTACGCATCACTACATTGGATCTG AACCTCGACTTTCTGGATCAGCC
CCasR3-RV	TGTATCGAGCGATGTACGAATACTCTTGCCGAGTCATAGCAGTGCAGTAGAGCCTGACCCGGATCT GAACCTCGACTTTCTGGATCAGCC
CCasR3FW	AATGTAGTGATGCGTAACCCAGGGATGTTAGCGCGTACTGAGGTACATAATAACATTTCACGCTCT AGCATGGAACCAAGACCCATGACG
CCasR4-FW	GGGTCAGGCTCTACTGCACTGCTATGACTCGGCAAGAGTATTCGTACATCGCTCGATACACGCTCTA GCATGGAACCAAGACCCATGACG
CCasR5-FW	GCTCTCAACAGTCACTTGTGTGCCAAAATATTATACCTACTTCATACATTTTCAATTAAGCGCTCTAG CATGGAACCAAGACCCATGACG
CCasR5-RV	TAATCTTACACTAGTTTATAAGTGTCACGAACGATGAAATGGAAACTTGGGGGGGAAGGCGGATCT GAACCTCGACTTTCTGGATCAGCC
CCasR1-FW	ACAAGTTGACGCGACTTCTGTAAAGTTTATTTACAAGATAACAAAGAAACTCCCTTAAGCCGCTCTA GCATGGAACCAAGACCCATGACG
CCasR4-RV	TGTTAATGAACAGAAAACGAACAATTGGTAGCAGTGTTTTATAATTGCGCCCACAAGTTTGGATCTG AACCTCGACTTTCTGGATCAGCC
CCasAga1-FW	GCGCAGAATAATGATCTATCATCAATAATTATCGTGAACTTTTCCAGTATTTACGTTCATGCATGGAA CCAAGACCCATGA
CCasAga1-RV	ATTAGTTAATCCCAACAATATTGTGAACAGGTAGGTAAAATGAGCGAAAGATAATGTCATACGAAT GTACTAATTAAAAGATCAGAAAA

Cellulosome primers	sequence
BGLI-fragA-fw	TAGTAATGCAGACACTTGCG
BGLI-fragA-rv	CAACAGCGGTCTACTGAATC
BGLI-fragB-fw	CACTAGCTCAGATTCAGTAGACC
BGLI-fragB-rv	CGAGATGGACCGCAAG
BGLI1-FW	TTTGGATCCGTCTAGATGAA
BGL1-RV	AAACTCGAGTACTAGTATTC
BGL1A-FW	TTTGGATCCGTCTAGATGAGATTTCCTTCAATTTTTAC
BGL1A-RV	AAACTCGAGTACTAGTACTAATAAGGTAGGTGGGGTA
CBHII1-FW	TTTGGATCCGTCTAGATGAA
CBHII1-RV	AAACTCGAGTACTAGTAACT
CIPA3A-FW	TTTGGATCCGTCTAGATGCA
CIPA3A-RV	AAAGTCGACCTCGAGTACTA
CIPA3B-FW	TTTGGATCCGTCTAGATGCAGTTACTTCGCTGTTT
CIPA3B-RV	AAACTCGAGTACTAGTATTAGTGATGGTGATGGTGATGTTCGAAGGGCCCATTCGAAT
CIPA3C-RV	AAAGTCGACCTCGAGTATCA
EGII1-FW	TTTGGATCCGTCTAGATGAA
EGII1-RV	AAACTCGAGTACTAGTAGAC
Bio-His-EG-FW1	TATTTGAATTCGCGGCCGCTTCTAGATGCATCATCACCATCACCATG
Bio-His-EG-RV1	TATTTCTGCAGCGGCCGCTACTAGTATTACTTTCTTGCGAGACACGAG
Bio-ss1-HEGII-FW1	TATTTGAATTCGCGGCCGCTTCTAGATGAAGGTTTTGATTGTCTTG
Int-ss1-HEGII-FW1	TTTGGATCCGTCTAGATGATGAAGGTTTTGATTGTCTTG
Int-ss1-HEGII-RV1	AAACTCGAGTACTAGTATTACTTTCTTGCGAGACACGAGC

PAL2 primers	sequence
PAL2A-FW	TTTGGATCCGTCTAGATGGA
PAL2A-RV	AAACTCGAGTACTAGTATTAGCAAATCGGAATCGGAGCTC
PAL2B-FW	TTTGGATCCATGCATCACCATCACCATCACGATCAAATCGAAGCAATGTT
PAL2B-RV	AAACTCGAGTACTAGTATTAATGGTGATGGTGATGGTGGCAAATCGGAATCGGAGC
PAL2C-FW	TTTGGATCCGTCTAGATGGATCAAATCGAAGCAAT
PAL2.1-FW	CACTAGCTCAGATTCAGTAG
PAL2.1-RV	AAACCATGGATAGCCTTGTT
PAL2.2-RV	TTAGCAGATTGGGATTGGGG
PAL2D-FW	ATATACCAGCATTTAAGAACCTAATGAGTTCTGTTTGTAATGCG
PAL2D-RV	AGGTTCTTAAATGCTGGTATATTCGGAAACACGAAGGAGA
Pal2F-fw	TTTGGATCCGTCTAGATGGATCAAATAGAAGCAAT
Pal2F-rv	AAACTCGAGTTAGTGATGGTGATGGTGATGGCAGATTGGGATTGGGGCAC
Pal2G-fw	TTTGGATCCATGCATCACCATCACCATCACATGGATCAAATAGAAGCAAT
Pal2G-rv	AAACTCGAGTACTAGTATTAGCAGATTGGGATTGGGG
PAL2-fragA-fw	TTTGGATCCGATGGATCAAATAGAAGCAATGTTG
PAL2-fragA-rv	AAACCATGGATAGCCTTGTTTC
PAL2-fragB-fw	ACTAGCTCAGATTCAGTAGACC
PAL2-fragB-rv	AAACTCGAGTTAGCAGATTGGGATTGGGG
P T7	GACCATCACACCACTGAAGACTGCGG
R T7	GTGATCATGAATTAATAAAAGTGTTCGC
PAL2-BB-fix-fw	TTAATGAATTCGCGGCCGCTTCTAGATGGACCAAATTGAGGCGATG
PAL2-BB-fix-rv	TTAATCTGCAGCGGCCGCTACTAGTACAGTTAGCAAATCGGAATCG
PAL2-BB-fw	GAATTCGCGGCCGCTTCTAGATGGACCAAATTGAGGCGATG
PAL2-BB-rv	CTGCAGCGGCCGCTACTAGTACAGTTAGCAAATCGGAATCG

Sequencing primers	sequence
genseqFW	GCAGACGACTCGAATAAG
genseqRV	AGCTCGTCAATAGTGGAGATTAC
VR primer fw	ATTACCGCCTTTGAGTGAGC
VR primer rv	TGCCACCTGACGTCTAAGAA
M13 fw	GTAAAACGACGGCCAGT
M13 rv	CAGGAAACAGCTATGAC
EGII-seq-fw	GGCTGTACCACAGATGG
EGII-seq-rv	GTTCTGTCGGAGCCAAG
BGL1-seq-paper-FW	GCAACAGCCAAGCATTAC
BGL1-seq2-paper-FW	ACCACAGCGAGGTTATTC
PAL2-seq-ver-RV	GTGGTGCTCATCAGTTTC
PAL2-seq-fw-internal	CTGCGTGGCACCATTAC

Zeocin cassette primers	sequence
Zcas1-FW	TATTTGAATTCGCGGCCGCTTCTAGAGTCCAGAAAGTCGAGGTTCAG
Zcas2-FW	TATTTGAATTCGCGGCCGCTTCTAGAGGGGCTGATCCAGAAAGTCGA
Zcas3-FW	TATTTGAATTCGCGGCCGCTTCTAGAGCCAGAAAGTCGAGGTTCAG
Zcas4-FW	TATTTGAATTCGCGGCCGCTTCTAGAGGATCCAGAAAGTCGAGGTTCAG
Zcas1-RV	TATTTCTGCAGCGGCCGCTACTAGTATTATGCTTCCGGCTCGTATG
Zcas2-RV	TATTTCTGCAGCGGCCGCTACTAGTACTTCCGGCTCGTATGTTGTG
Zcas3-RV	TATTTCTGCAGCGGCCGCTACTAGTAGCTCGGAATTAACCCTCAC

Synthetic DNA fragments

Synthetic DNA sequences	Source
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"

Plasmids

Plasmids	Source
pYD1-CipA3-EGII	From Wen et al. 2010
pYD1-CipA1-EGII	From Wen et al. 2010
pRS425-CBHII-BGL1	From Wen et al. 2010
p414 KanMX TEF1-Cas9-Tcyc	"Molmic group, RUG"
pMEL16 OR1	"Molmic group, RUG"
pMEL16-ARO10tar	This work
pMEL16-AGA2tar	This work
pMEL16-AGA1tar	This work
pUC57-PAL2	"Roelfes group, RUG"
pRS313+ s promHxt7-MCS-terHxt7	"Molmic group, RUG"
pRS313-Hxt7-PAL2	This work

Saccharomyces cerevisiae strains

Strains	Source
BJ1991	"Molecular Cell Biology group, RUG"
BY4741	"Molmic group, RUG"
BJC3CB	This work
BJC1CB	This work
YPH499	"Molecular Cell Biology group, RUG"
YPHPAL2	This work
YPHCON	This work

@@ Line 18: / Line 18: @@
 <img src="https://static.igem.org/mediawiki/2018/8/85/T--Groningen--banner_primers.png" class="responsive-img">
+     <h4>Primers, plasmids, and strains used during this project</h4>
       <br>
+     <h5>Primers</h5>
       <table><tr><th>CRISPR-Cas Primers</th><th>sequence</th></tr><tr><td>588 FW</td><td>CTTGAAAACTTACGCTCATCTCTTCGACG</td></tr><tr><td>589 RV</td><td>CGGACTTAAGAAAATCCAGGATTGTCTTTCC</td></tr><tr><td>6006 FW</td><td>GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTC</td></tr><tr><td>6005 RV</td><td>GATCATTTATCTTTCACTGCGGAGAAG</td></tr><tr><td>F ARO10 tar</td><td>TGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCAATATACGAACGAAA<br>CAATGGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC</td></tr><tr><td>R ARO10 tar</td><td>GTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACCATTGTTTCGTTCGTATA<br>TTGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA</td></tr><tr><td>F AGA2 KO tar</td><td>TGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCAAAACATACTGTGTGT<br>TTATGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC</td></tr><tr><td>R AGA2 KO tar</td><td>GTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACATAAACACACAGTATGT<br>TTTGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA</td></tr><tr><td>F AGA1 OE tar</td><td>TGCGCATGTTTCGGCGTTCGAAACTTCTCCGCAGTGAAAGATAAATGATCTTACGTTCATCTTTGAA<br>AAAGTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAAC</td></tr><tr><td>R AGA1 OE tar</td><td>GTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAACTTTTTCAAAGATGAACGT<br>AAGATCATTTATCTTTCACTGCGGAGAAGTTTCGAACGCCGAAACATGCGCA</td></tr><tr><td>CCasR1-RV</td><td>CGTGTAATCTGTGACAATTTCGATGCGTACACTGCGGCCCCGAAGTAGCATAGCTTATCTGGATCTG<br>AACCTCGACTTTCTGGATCAGCC</td></tr><tr><td>CCasR2-FW</td><td>AGATAAGCTATGCTACTTCGGGGCCGCAGTGTACGCATCGAAATTGTCACAGATTACACGCGCTCT<br>AGCATGGAACCAAGACCCATGACG</td></tr><tr><td>CCasR2-RV</td><td>TGAAATGTTATTATGTACCTCAGTACGCGCTAACATCCCTGGGTTACGCATCACTACATTGGATCTG<br>AACCTCGACTTTCTGGATCAGCC</td></tr><tr><td>CCasR3-RV</td><td>TGTATCGAGCGATGTACGAATACTCTTGCCGAGTCATAGCAGTGCAGTAGAGCCTGACCCGGATCT<br>GAACCTCGACTTTCTGGATCAGCC</td></tr><tr><td>CCasR3FW</td><td>AATGTAGTGATGCGTAACCCAGGGATGTTAGCGCGTACTGAGGTACATAATAACATTTCACGCTCT<br>AGCATGGAACCAAGACCCATGACG</td></tr><tr><td>CCasR4-FW</td><td>GGGTCAGGCTCTACTGCACTGCTATGACTCGGCAAGAGTATTCGTACATCGCTCGATACACGCTCTA<br>GCATGGAACCAAGACCCATGACG</td></tr><tr><td>CCasR5-FW</td><td>GCTCTCAACAGTCACTTGTGTGCCAAAATATTATACCTACTTCATACATTTTCAATTAAGCGCTCTAG<br>CATGGAACCAAGACCCATGACG</td></tr><tr><td>CCasR5-RV</td><td>TAATCTTACACTAGTTTATAAGTGTCACGAACGATGAAATGGAAACTTGGGGGGGAAGGCGGATCT<br>GAACCTCGACTTTCTGGATCAGCC</td></tr><tr><td>CCasR1-FW</td><td>ACAAGTTGACGCGACTTCTGTAAAGTTTATTTACAAGATAACAAAGAAACTCCCTTAAGCCGCTCTA<br>GCATGGAACCAAGACCCATGACG</td></tr><tr><td>CCasR4-RV</td><td>TGTTAATGAACAGAAAACGAACAATTGGTAGCAGTGTTTTATAATTGCGCCCACAAGTTTGGATCTG<br>AACCTCGACTTTCTGGATCAGCC</td></tr><tr><td>CCasAga1-FW</td><td>GCGCAGAATAATGATCTATCATCAATAATTATCGTGAACTTTTCCAGTATTTACGTTCATGCATGGAA<br>CCAAGACCCATGA</td></tr><tr><td>CCasAga1-RV</td><td>ATTAGTTAATCCCAACAATATTGTGAACAGGTAGGTAAAATGAGCGAAAGATAATGTCATACGAAT<br>GTACTAATTAAAAGATCAGAAAA</td></tr></table>
       <div class="clear"></div>
@@ Line 38: / Line 40: @@
       <div class="clear"></div><p> </p>
 <br>
+    <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>
       <div class="clear"></div><p> </p>
 <br>
-      <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>
+<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>
       <div class="clear"></div><p> </p>
 <br>
-     <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>
+<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>
       <div class="clear"></div><p> </p>