User talk:Nkuldell/SAGA swap pt 2: Difference between revisions
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5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA | 5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA | ||
agattgtactgagagtgcac | agattgtactgagagtgcac | ||
==Sequence/strain details== | |||
===1. K/O primers to put URA3 in SGF73=== | |||
NOxxx | |||
*sgf73_URA3_KO_fwd | |||
*5' TGAACACACAAGAGAAGCGCAAAAGAGTAAAGAGCTAAAatgtcgaaagctacatataa | |||
*LENGTH: 59 | |||
*GC CONTENT: 35.6 % | |||
*MELT TEMP: 66.0 ºC <br> | |||
NOxxx | |||
*sgf73_URA3_KO_rev | |||
*5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA ttagttttgctggccgcatc | |||
*LENGTH: 59 | |||
*GC CONTENT: 45.8 % | |||
*MELT TEMP: 69.2 º | |||
===URA3 from pRS416 according to NEB site=== | |||
1 A TGTCGAAAGC TACATATAAG GAACGTGCTG CTACTCATCC <br> | |||
451 TAGTCCTGTT GCTGCCAAGC TATTTAATAT CATGCACGAA AAGCAAACAA <br> | |||
501 ACTTGTGTGC TTCATTGGAT GTTCGTACCA CCAAGGAATT ACTGGAGTTA <br> | |||
551 GTTGAAGCAT TAGGTCCCAA AATTTGTTTA CTAAAAACAC ATGTGGATAT <br> | |||
601 CTTGACTGAT TTTTCCATGG AGGGCACAGT TAAGCCGCTA AAGGCATTAT <br> | |||
651 CCGCCAAGTA CAATTTTTTA CTCTTCGAAG ACAGAAAATT TGCTGACATT <br> | |||
701 GGTAATACAG TCAAATTGCA GTACTCTGCG GGTGTATACA GAATAGCAGA <br> | |||
751 ATGGGCAGAC ATTACGAATG CACACGGTGT GGTGGGCCCA GGTATTGTTA <br> | |||
801 GCGGTTTGAA GCAGGCGGCA GAAGAAGTAA CAAAGGAACC TAGAGGCCTT <br> | |||
851 TTGATGTTAG CAGAATTGTC ATGCAAGGGC TCCCTATCTA CTGGAGAATA <br> | |||
901 TACTAAGGGT ACTGTTGACA TTGCGAAGAG CGACAAAGAT TTTGTTATCG <br> | |||
951 GCTTTATTGC TCAAAGAGAC ATGGGTGGAA GAGATGAAGG TTACGATTGG <br> | |||
1001 TTGATTATGA CACCCGGTGT GGGTTTAGAT GACAAGGGAG ACGCATTGGG <br> | |||
1051 TCAACAGTAT AGAACCGTGG ATGATGTGGT CTCTACAGGA TCTGACATTA <br> | |||
1101 TTATTGTTGG AAGAGGACTA TTTGCAAAGG GAAGGGATGC TAAGGTAGAG <br> | |||
1151 GGTGAACGTT ACAGAAAAGC AGGCTGGGAA GCATATTTGA GAAGATGCGG <br> | |||
1201 CCAGCAAAAC TAA<br> |
Revision as of 11:58, 6 July 2006
Emailed info
1. From: Mark Hickman
Subject: Re: memory lapses... Date: Sun, 11 Jun 2006 21:32:42 -0400
SGF73 is required for the induction of the PAU genes under hypoxic conditions. As far as I know, this is the first transcriptional defect seen for sgf73 mutants. Otherwise, nothing is known about its function. Dom worked on human Sgf73 for his PhD thesis; he found it was subject to glutamine expansion. One of my plans for the future was to check whether sgf73 deletion has a phenotype, especially under hypoxic conditions (since there might be a consequence to the PAU genes not being induced). Another idea was to do a synthetic lethal screen with sgf73 under aerobic and hypoxic conditions.
We have the cerevisiae sgf73 deletion strain (I have worked with FY2475). Not sure if there is a cDNA, but Fred or Lisa might know.
Let me know if you have any other questions. You could also ask Dom about pombe sgf73+. He might be knocking that out and/or have a cDNA.
Thanks for the anniversary wishes! It's July 31. I guess we are still newlyweds until the first year?
Good luck with your son's surgery. I have a memory lapse too: your son's name.
See you soon Mark
2. From: Mark Hickman
Subject: Re: memory lapses... Date: Fri, 23 Jun 2006 11:25:35 -0400
Natalie,
No problem! Just got back from Venice. How did it go with Spencer?
It's MAT alpha ura3-52 lys2-173R2 leu2D1 arg4-12 sgf73D0::kanMX his4-917d. I am assuming it's a clean ORF deletion but not sure. It should be in Jenny's notebook, or maybe Lisa knows? Won't you need to put in URA3, so you can do the swap with 5FOA?
Do you know about the Winston Lab yeast strains on the web? http://genepath.med.harvard.edu/strainfinder/yeast.php
Lisa is still in the lab. Not much longer though....
Mark
3. From: Mark Hickman
Subject: Re: memory lapses... Date: Fri, 23 Jun 2006 11:49:41 -0400
Natalie, I just happened to come across a file (totally randomly!) with Jenny's knockout primers:
Sgf73 JW109 left primer
5' TGAACACACAAGAGAAGCGCAAAAGAGTAAAGAGCTAAA ctgtgcggtatttcacaccg
JW110 right primer 5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA agattgtactgagagtgcac
Sequence/strain details
1. K/O primers to put URA3 in SGF73
NOxxx
- sgf73_URA3_KO_fwd
- 5' TGAACACACAAGAGAAGCGCAAAAGAGTAAAGAGCTAAAatgtcgaaagctacatataa
- LENGTH: 59
- GC CONTENT: 35.6 %
- MELT TEMP: 66.0 ºC
NOxxx
- sgf73_URA3_KO_rev
- 5' CTCACTTCGTGAACATGCTGGATAACGTGCATGATTCAA ttagttttgctggccgcatc
- LENGTH: 59
- GC CONTENT: 45.8 %
- MELT TEMP: 69.2 º
URA3 from pRS416 according to NEB site
1 A TGTCGAAAGC TACATATAAG GAACGTGCTG CTACTCATCC
451 TAGTCCTGTT GCTGCCAAGC TATTTAATAT CATGCACGAA AAGCAAACAA
501 ACTTGTGTGC TTCATTGGAT GTTCGTACCA CCAAGGAATT ACTGGAGTTA
551 GTTGAAGCAT TAGGTCCCAA AATTTGTTTA CTAAAAACAC ATGTGGATAT
601 CTTGACTGAT TTTTCCATGG AGGGCACAGT TAAGCCGCTA AAGGCATTAT
651 CCGCCAAGTA CAATTTTTTA CTCTTCGAAG ACAGAAAATT TGCTGACATT
701 GGTAATACAG TCAAATTGCA GTACTCTGCG GGTGTATACA GAATAGCAGA
751 ATGGGCAGAC ATTACGAATG CACACGGTGT GGTGGGCCCA GGTATTGTTA
801 GCGGTTTGAA GCAGGCGGCA GAAGAAGTAA CAAAGGAACC TAGAGGCCTT
851 TTGATGTTAG CAGAATTGTC ATGCAAGGGC TCCCTATCTA CTGGAGAATA
901 TACTAAGGGT ACTGTTGACA TTGCGAAGAG CGACAAAGAT TTTGTTATCG
951 GCTTTATTGC TCAAAGAGAC ATGGGTGGAA GAGATGAAGG TTACGATTGG
1001 TTGATTATGA CACCCGGTGT GGGTTTAGAT GACAAGGGAG ACGCATTGGG
1051 TCAACAGTAT AGAACCGTGG ATGATGTGGT CTCTACAGGA TCTGACATTA
1101 TTATTGTTGG AAGAGGACTA TTTGCAAAGG GAAGGGATGC TAAGGTAGAG
1151 GGTGAACGTT ACAGAAAAGC AGGCTGGGAA GCATATTTGA GAAGATGCGG
1201 CCAGCAAAAC TAA