User:Nkuldell/SAGA swap pt 2 - Revision history

Nkuldell: /* BBa_Y00029 [http://parts.mit.edu/registry/index.php/Part:BBa_Y00029] */

2006-09-15T18:13:05Z

<b> BBa_Y00029</b> [http://parts.mit.edu/registry/index.php/Part:BBa_Y00029]

←Older revision		Revision as of 18:13, 15 September 2006
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	===<b> BBa_Y00029</b> [http://parts.mit.edu/registry/index.php/Part:BBa_Y00029]===		===<b> BBa_Y00029</b> [http://parts.mit.edu/registry/index.php/Part:BBa_Y00029]===
	Message to DNA 2.0:		Message to DNA 2.0:
-	<br>The gene is an S. pombe gene called SPBC1921.07c. The protein sequence is:	+	<br>The gene is an S. pombe gene called SPBC1921.07c [[http://www.genedb.org/genedb/Search?organism=pombe&name=SPBC1921.07c]]. The protein sequence is:
	<br>		<br>
	mvrpinaeed vtsmwvkfhe slnpirssli kqeecyktvd gddnpieeri kacdagiqts		mvrpinaeed vtsmwvkfhe slnpirssli kqeecyktvd gddnpieeri kacdagiqts
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	optimized the cloning sites can be added by tagging the 5' end before		optimized the cloning sites can be added by tagging the 5' end before
	the ATG with: GTTTCTTCGAATTCGCGGCCGCTTCTAGAG and tagging the 3' end after the stop with: TACTAGTAGCGGCCGCTGCAGGAAGAAAC.		the ATG with: GTTTCTTCGAATTCGCGGCCGCTTCTAGAG and tagging the 3' end after the stop with: TACTAGTAGCGGCCGCTGCAGGAAGAAAC.
-

	===Primers===		===Primers===

Nkuldell: /* DNA Reagents */

2006-09-15T17:53:03Z

DNA Reagents

←Older revision		Revision as of 17:53, 15 September 2006
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	===<b> BBa_Y00073 </b>[http://parts.mit.edu/r/parts/partsdb/part_info.cgi?id=6842] ===		===<b> BBa_Y00073 </b>[http://parts.mit.edu/r/parts/partsdb/part_info.cgi?id=6842] ===
	had DNA 2.0 codon-optimize S. pombe gene SPCC126.04c [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=NP_588447.1]]		had DNA 2.0 codon-optimize S. pombe gene SPCC126.04c [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=NP_588447.1]]
-	including biobrick ends for expression of ORF in S. cerevisiae	+	[[http://www.genedb.org/genedb/Search?organism=pombe&name=SPCC126.04c&isid=true]]including biobrick ends for expression of ORF in S. cerevisiae
	This subunit is homolog of S. cerevisiae SGF73 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf73]] subunit of SAGA and deletion of this subunit in S. cerevisiae results in viable cells but no induction of PAU genes under hypoxic conditions.		This subunit is homolog of S. cerevisiae SGF73 [[http://db.yeastgenome.org/cgi-bin/locus.pl?locus=sgf73]] subunit of SAGA and deletion of this subunit in S. cerevisiae results in viable cells but no induction of PAU genes under hypoxic conditions.

Nkuldell: /* Phenotype wt vs sgf73 vs sgf29 vs double */

2006-09-10T11:23:42Z

Phenotype wt vs sgf73 vs sgf29 vs double

←Older revision		Revision as of 11:23, 10 September 2006
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	[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes YPED.jpg\|thumb\|left\|YPEG]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes YPED.jpg\|thumb\|left\|YPEG]]
	[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes 3%form.jpg\|thumb\|left\|3%form]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes 3%form.jpg\|thumb\|left\|3%form]]
		+	[[Image:Macintosh HD-Users-nkuldell-Desktop-SAGAswap txdPCRprod.jpg\|thumb\|left\|1/10th txd PCR products]]

Nkuldell at 19:41, 25 August 2006

2006-08-25T19:41:46Z

←Older revision		Revision as of 19:41, 25 August 2006
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	**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°		**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°

-	*SpSGF73_ATG_fwd (~~NOxxx~~)	+	*SpSGF73_ATG_fwd (NO126)
	**use with NO108 to confirm sequence from pombe is in cerevisiae		**use with NO108 to confirm sequence from pombe is in cerevisiae
	**binds 5' end of Sp homolog of SGF73		**binds 5' end of Sp homolog of SGF73
	**5'-atgttaacag aacaacagac tttggagtta		**5'-atgttaacag aacaacagac tttggagtta

-	SpSGF73_ATG_fwd (~~NOxxx~~)	+	SpSGF73_ATG_fwd (NO127)
	**use with NO108 to confirm sequence from pombe is in cerevisiae		**use with NO108 to confirm sequence from pombe is in cerevisiae
	**binds 5' end of codon optimized version of Sp homolog of SGF73		**binds 5' end of codon optimized version of Sp homolog of SGF73
	**5'-ATGCTAACAGAACAACAAACACTTGAACTATTCCCCG		**5'-ATGCTAACAGAACAACAAACACTTGAACTATTCCCCG

-	SpSGF29_ATG_fwd (~~NOxxx~~)	+	SpSGF29_ATG_fwd (NO128)
	**use with NO110 to confirm sequence from pombe is in cerevisiae		**use with NO110 to confirm sequence from pombe is in cerevisiae
	**binds 5' end of codon optimized version of Sp homolog of SGF29		**binds 5' end of codon optimized version of Sp homolog of SGF29

Nkuldell: /* Primers */

2006-08-18T20:39:12Z

Primers

←Older revision		Revision as of 20:39, 18 August 2006
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	**5'- ATC ACT TCC GAC GAT ACC AAA ATA ATG ACA AAA TGC CAT G agaagatcttatgatatgta		**5'- ATC ACT TCC GAC GAT ACC AAA ATA ATG ACA AAA TGC CAT G agaagatcttatgatatgta
	**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°		**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°
		+
		+	*SpSGF73_ATG_fwd (NOxxx)
		+	**use with NO108 to confirm sequence from pombe is in cerevisiae
		+	**binds 5' end of Sp homolog of SGF73
		+	**5'-atgttaacag aacaacagac tttggagtta
		+
		+	SpSGF73_ATG_fwd (NOxxx)
		+	**use with NO108 to confirm sequence from pombe is in cerevisiae
		+	**binds 5' end of codon optimized version of Sp homolog of SGF73
		+	**5'-ATGCTAACAGAACAACAAACACTTGAACTATTCCCCG
		+
		+	SpSGF29_ATG_fwd (NOxxx)
		+	**use with NO110 to confirm sequence from pombe is in cerevisiae
		+	**binds 5' end of codon optimized version of Sp homolog of SGF29
		+	**5'-ATG GTT AGA CCT ATA AAT GCC GAA GAA GAT

	==Yeast Strains==		==Yeast Strains==

Nkuldell: /* Primers */

2006-08-18T13:44:44Z

Primers

←Older revision		Revision as of 13:44, 18 August 2006
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	**if used on PCR product of NO112, NO113 or NO115 then Tm of landing is 53.9°		**if used on PCR product of NO112, NO113 or NO115 then Tm of landing is 53.9°

-	*upstmSGF29_150bp_fwd (~~NOxxx~~)	+	*upstmSGF29_150bp_fwd (NO124)
	**5'-GTT AAA GAC ACA ATA CCT TGG TGG CTT CTC TAA GTG GGG G gagtttttcacagcaaaaca		**5'-GTT AAA GAC ACA ATA CCT TGG TGG CTT CTC TAA GTG GGG G gagtttttcacagcaaaaca
	**if used on PCR product of NO116 or NO120 then Tm of landing is 49.5°		**if used on PCR product of NO116 or NO120 then Tm of landing is 49.5°

-	*dwstmSGF29_150bp_rev (~~NOxxx~~)	+	*dwstmSGF29_150bp_rev (NO125)
	**5'- ATC ACT TCC GAC GAT ACC AAA ATA ATG ACA AAA TGC CAT G agaagatcttatgatatgta		**5'- ATC ACT TCC GAC GAT ACC AAA ATA ATG ACA AAA TGC CAT G agaagatcttatgatatgta
	**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°		**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°

Nkuldell: /* Primers */

2006-08-15T10:23:35Z

Primers

←Older revision		Revision as of 10:23, 15 August 2006
Line 67:		Line 67:
	*SpSGF29toSc_fwd (to amplify Sp genomic sequence for SPBC1921.07c = Sc homolog of Sc SGF29) (NO116)		*SpSGF29toSc_fwd (to amplify Sp genomic sequence for SPBC1921.07c = Sc homolog of Sc SGF29) (NO116)
	**5' GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggtacgcgggataaatg		**5' GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggtacgcgggataaatg
-	**third base should be G not C (fixed on extending oligo	+	**third base should be G not C (fixed on extending oligo "upstmSGF29_150bp_fwd")
	**landing seq has Tm of 52.5°		**landing seq has Tm of 52.5°
	*SpSGF29toSc_rev (NO117)		*SpSGF29toSc_rev (NO117)
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	SpSGF29toSc_fwd (where * indicates codon optimized version of Sp homolog of the Sc SGF29) (NO120)		SpSGF29toSc_fwd (where * indicates codon optimized version of Sp homolog of the Sc SGF29) (NO120)
	**GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggttagacctataaatgc		**GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggttagacctataaatgc
-	**third base should be G not C (fixed on extending oligo "upstmSGF29_150bp_fwd"	+	**third base should be G not C (fixed on extending oligo "upstmSGF29_150bp_fwd")
	**landing seq has Tm of 46.9°		**landing seq has Tm of 46.9°
	SpSGF29toSc_rev (NO121)		SpSGF29toSc_rev (NO121)
Line 104:		Line 104:

	*dwstmSGF29_150bp_rev (NOxxx)		*dwstmSGF29_150bp_rev (NOxxx)
-	**5'-	+	**5'- ATC ACT TCC GAC GAT ACC AAA ATA ATG ACA AAA TGC CAT G agaagatcttatgatatgta
-	**if used on PCR product of NO117 or NO121 then Tm of landing is °	+	**if used on PCR product of NO117 or NO121 then Tm of landing is 42.0°

	==Yeast Strains==		==Yeast Strains==

Nkuldell: /* Primers */

2006-08-15T10:09:27Z

Primers

←Older revision		Revision as of 10:09, 15 August 2006
Line 67:		Line 67:
	*SpSGF29toSc_fwd (to amplify Sp genomic sequence for SPBC1921.07c = Sc homolog of Sc SGF29) (NO116)		*SpSGF29toSc_fwd (to amplify Sp genomic sequence for SPBC1921.07c = Sc homolog of Sc SGF29) (NO116)
	**5' GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggtacgcgggataaatg		**5' GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggtacgcgggataaatg
		+	**third base should be G not C (fixed on extending oligo
	**landing seq has Tm of 52.5°		**landing seq has Tm of 52.5°
	*SpSGF29toSc_rev (NO117)		*SpSGF29toSc_rev (NO117)
Line 83:		Line 84:

	SpSGF29toSc_fwd (where * indicates codon optimized version of Sp homolog of the Sc SGF29) (NO120)		SpSGF29toSc_fwd (where * indicates codon optimized version of Sp homolog of the Sc SGF29) (NO120)
-	**GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggttagacctataaatgc	+	**GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggttagacctataaatgc
		+	**third base should be G not C (fixed on extending oligo "upstmSGF29_150bp_fwd"
	**landing seq has Tm of 46.9°		**landing seq has Tm of 46.9°
	SpSGF29toSc_rev (NO121)		SpSGF29toSc_rev (NO121)
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	**if used on PCR product of NO112, NO113 or NO115 then Tm of landing is 53.9°		**if used on PCR product of NO112, NO113 or NO115 then Tm of landing is 53.9°

		+	*upstmSGF29_150bp_fwd (NOxxx)
		+	**5'-GTT AAA GAC ACA ATA CCT TGG TGG CTT CTC TAA GTG GGG G gagtttttcacagcaaaaca
		+	**if used on PCR product of NO116 or NO120 then Tm of landing is 49.5°
		+
		+	*dwstmSGF29_150bp_rev (NOxxx)
		+	**5'-
		+	**if used on PCR product of NO117 or NO121 then Tm of landing is °

	==Yeast Strains==		==Yeast Strains==

Nkuldell at 18:30, 11 August 2006

2006-08-11T18:30:33Z

←Older revision		Revision as of 18:30, 11 August 2006
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	**landing seq has Tm of 43.2 °		**landing seq has Tm of 43.2 °

-	*upstmSGF73_150bp_fwd (~~NOxxx~~)	+	*upstmSGF73_150bp_fwd (NO122)
	**5'- TAA TTT ACC AAA ACG GAA TAA ACC AAA AAA ATA AGA ATA Gtg aac aca caa gag aag cgc		**5'- TAA TTT ACC AAA ACG GAA TAA ACC AAA AAA ATA AGA ATA Gtg aac aca caa gag aag cgc
	**if used on PCR product of NO111 or NO114 then Tm of landing is 55.8°		**if used on PCR product of NO111 or NO114 then Tm of landing is 55.8°

-	*dwstmSGF73_150bp_rev (~~NOxxx~~)	+	*dwstmSGF73_150bp_rev (NO123)
	**5'- TAG ACG TGT ACA TGT TAC TTC GGC GAA TAA TTT TTT ATT Act cac ttc gtg aac atg ctg		**5'- TAG ACG TGT ACA TGT TAC TTC GGC GAA TAA TTT TTT ATT Act cac ttc gtg aac atg ctg
	**if used on PCR product of NO112, NO113 or NO115 then Tm of landing is 53.9°		**if used on PCR product of NO112, NO113 or NO115 then Tm of landing is 53.9°

Nkuldell at 18:56, 8 August 2006

2006-08-08T18:56:07Z

←Older revision		Revision as of 18:56, 8 August 2006
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	**landing seq has Tm of 43.7°		**landing seq has Tm of 43.7°

-	*SpSGF29ck_rev (~~Nxxx~~)	+	*SpSGF29ck_rev (NO119)
	**use with NO109 to confirm sequence from pombe is in cerevisiae, expecting 821bp product		**use with NO109 to confirm sequence from pombe is in cerevisiae, expecting 821bp product
	**binds 3' end of Sp homolog of SGF29		**binds 3' end of Sp homolog of SGF29
	**5' TTA ACC ATT GTA CTC TAA CAC CAA A		**5' TTA ACC ATT GTA CTC TAA CAC CAA A

-	*SpSGF29ck_fwd (~~Nxxx~~)	+	*SpSGF29ck_fwd (NO118)
	**use with NO110 to confirm sequence from pombe is in cerevisiae, expecting 821bp product		**use with NO110 to confirm sequence from pombe is in cerevisiae, expecting 821bp product
	**binds 5' end of Sp homolog of SGF29		**binds 5' end of Sp homolog of SGF29
	**5' ATG GTA CGC CCC ATA AAT GCT G		**5' ATG GTA CGC CCC ATA AAT GCT G

-	SpSGF29toSc_fwd (where * indicates codon optimized version of Sp homolog of the Sc SGF29) (~~NOxxx~~)	+	SpSGF29toSc_fwd (where * indicates codon optimized version of Sp homolog of the Sc SGF29) (NO120)
	**GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggttagacctataaatgc		**GACTTTTTCACAGCAAAACACACGGTCACCTTTCTTATTatggttagacctataaatgc
	**landing seq has Tm of 46.9°		**landing seq has Tm of 46.9°
-	SpSGF29toSc_rev (~~NOxxx~~)	+	SpSGF29toSc_rev (NO121)
	**AGAAGATCTTATGATATGTAGTAAATGTTAACCACCATTttatccattgtactctaaaa		**AGAAGATCTTATGATATGTAGTAAATGTTAACCACCATTttatccattgtactctaaaa
	**landing seq has Tm of 43.2 °		**landing seq has Tm of 43.2 °

←Older revision		Revision as of 11:23, 10 September 2006
Line 360:		Line 360:
	[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes YPED.jpg\|thumb\|left\|YPEG]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes YPED.jpg\|thumb\|left\|YPEG]]
	[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes 3%form.jpg\|thumb\|left\|3%form]]		[[Image:Macintosh HD-Users-nkuldell-Desktop-ptypes 3%form.jpg\|thumb\|left\|3%form]]
		+	[[Image:Macintosh HD-Users-nkuldell-Desktop-SAGAswap txdPCRprod.jpg\|thumb\|left\|1/10th txd PCR products]]