BerkiGEM2007 AllConstructionFiles

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Revision as of 01:46, 6 June 2007

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Complete list of construction files

Note on use: put your construction files in your own construction file template file. These link from your notebook page. They will automatically appear on this page.

Austin
1128 RBS Libraries:
pBca1101-I716051 (built): Kan cassette RBS pool
pBca1101-I716052(built): Cmr cassette RBS pool

Unmutated basic parts:
9145-I716053(built): alpha HbA in 9145(biobricks 2.0 format)
9145-I716054(built): beta HbA in 9145(biobricks 2.0 format)
9145-I716055(built): AHSP in 9145(biobricks 2.0 format)

Cassette Construction Using 1128 RBS Library:
9145-I716056(built): -kan-RBS library-alpha HbA-
9145-I716057(built): -CmR-RBS library-beta HbA-
9145-I716060(built): beta-alpha cassette (with RBS libraries)

9145-I716065(built): 2X mutant -Kan-rbs-alpha Hba (L29F and V96W)
9145-I716066(built): 2X mutant -Cmr-beta Hba (Asn108Lys and Lys82Asp)
9145-I716067(built): 2X mutants -rbs library-beta-rbs library-alpha- (with RBS libraries)

9145-I716061(built): pTRC-rbs-beta-rbs-alpha
pTrc-I716069(built): 2X mutant -pTRC-rbs-2x beta-rbs-2x alpha L29F/V96W and Asn108Lys/Lys82Asp

HbA Subunit Mutant Variants:
9145-I716058(built): 1X mutant HbA alpha (L29F) AKA: I716053m29
9145-I716059(built): 1X mutant HbA beta (Asn108Lys "Presbyterian") AKA: I716054m108
9145-I716062(built): 2X mutant HbA alpha (L29F/V96W) AKA: I716053m29m96
9145-I716063(built): 2X mutant HbA beta (Asn108Lys/Lys82Asp "Providence/Presbyterian") AKA: I716054m108m82
9145-I716072(built): 1X mutant beta Hba (Lys82Asp "Providence")
9145-I716073(built): unmutated Di-alpha fusion, biobricked
9145-I716068(built): 2X mutant Di-Alpha fusion, biobricked

No Scar Rbs-Part RBS library
1103-I716064: -pCon-(no scar site)-rbs-beta-rbs-alpha

9145-I716070(built): alpha HbA-TT
9145-I716077(built): Unmutated Di-Alpha fusion - TT
9145-I716078(built): 2X mutant alpha - TT
9145-I716079(built): 2X mutant Di-alpha fusion -TT

9145-I716080(built): -rbs-(no scar)-beta
9145-I716081(built): -rbs-(no scar)-1X mutant beta (providence Lys82Asp)
9145--I716082(built): -rbs-(no scar)-2X mutant beta (providence/Presbyterian Lys82Asp/Asn108Lys)

9145-I716071(built): -rbs lib-(NO SCAR)-beta-rbs lib-(no scar)-alpha-TT
9145-I716074(built): -rbs lib-(NO SCAR)-beta 1X mutant, providence (Lys82Asp) - rbs lib-(no scar) - unmutated di-alpha-TT- (Best Yield)
9145-I716075(built): -rbs lib-(NO SCAR)-beta 2X mutant, providence (Lys82Asp) and Presbyterian (Asn108Lys)-rbs lib-(no scar) - unmutated di alpha - TT- (Best all around)
9145-I716076(built): -rbs lib-(NO SCAR)-1X mutant beta, presbyterian (Asn108Lys)-rbs lib-(no scar)-2X mutant alpha (L29F and V96W) - TT (Second best all around)

9145-I716083(built): pT7105-rbs lib-(NO SCAR)-beta-rbs lib-(no scar)-alpha-TT
9145-I716084(built): pT7105-rbs lib-(NO SCAR)-beta 1X mutant, providence (Lys82Asp) - rbs lib-(no scar) - unmutated di-alpha-TT- (Best Yield)
9145-I716085(built): pT7105-rbs lib-(NO SCAR)-beta 2X mutant, providence (Lys82Asp) and Presbyterian (Asn108Lys)-rbs lib-(no scar) - unmutated di alpha - TT- (Best all around)
9145-I716086(built): pT7105-rbs lib-(NO SCAR)-1X mutant beta, presbyterian (Asn108Lys)-rbs lib-(no scar)-2X mutant alpha (L29F and V96W) - TT (Second best all around)

petDUET stuffs beta insertion

9145-I716087(built): (unmodified beta)insertion
9145-I716088(built): (Beta providence) insertion
9145-I716089(built): (Beta providence / Presbyterian) insertion
9145-I716090(built): (Beta presbyterian) insertion

petDUET stuffs alpha and beta insertion

9145-I716091(built): unmodified beta + unmodified alpha: "Unmodified" in petDUET
9145-I716092: Beta providence + unmodified dialpha fusion: "Best Yield" in petDUET
9145-I716093(built): Beta providence / Presbyterian + unmodified dialpha fusion : "Best All Around" in petDUET
9145-I716094(built): Beta presbyterian + 2X mutant alpha L29F/V96W: "Second Best All Around" in petDUET

(Basically Biobricked)Hemoglobin cassette + hemA/hemB:

9145-I716095 (built): "Unmodified" (I716091) + hemA/hemB cassette
9145-I716096 (built): "Best Yield" (I716092) + hemA/hemB cassette
9145-I716097 (built): "Best All Around" (I716093) + hemA/hemB cassette
9145-I716098: "Second Best All Around" (I716094) + hemA/hemB cassette

(Basically Biobricked)Hemoglobin cassette + Cytochrome B5/B5 reductase cassette + hemA/hemB cassette:

9145-I716099(built): "Unmodified" (I716091) + cytochrome b5/b5reductase cassette + hemA/hemB cassette
9145-I716100: "Best Yield" (I716092) + cytochrome b5/b5 reductase cassette + hemA/hemB cassette
9145-I716351(built): "Best All Around" (I716093) + cytochrome b5/b5 reductase cassette + hemA/hemB cassette
9145-I716352: "Second Best All Around" (I716094) + cytochrome b5/b5reductase cassette + hemA/hemB cassette

(Basically Biobricked)Hemoglobin cassette + cytochrome b5/b5 reductase + hemA/hemB + sodC/katG cassette:

9145-I716358: "Unmodified" (I716091) + cytochrome b5/b5reductase cassette + hemA/hemB cassette + sodC/KatG
9145-I716359: "Best Yield" (I716092) + cytochrome b5/b5 reductase cassette + hemA/hemB cassette + sodC/katG
9145-I716360: "Best All Around" (I716093) + cytochrome b5/b5 reductase cassette + hemA/hemB cassette + sodC/KatG
9145-I716361: "Second Best All Around" (I716094) + cytochrome b5/b5reductase cassette + hemA/hemB cassette + sodC/KatG

Detox constructs
9145-I716353: AdhE in petDUET

Biobricked petDUET Hemoglobin Cassettes (XhoI/EcoRI/BglII sites removed)
9145-I716354: "Unmodified" (I716091)
9145-I716355: "Best Yield" (I716092)
9145-I716356: "Best All Around" (I716093)
9145-I716357: "Second Best All Around" (I716094)

Different T7's with Hem Genes
9145-I716366: T7 Clone A with Hem genes A + B
9145-I716367: T7 Clone C with Hem genes A + B

Biobricked petDUET Hemoglobin Cassettes + sodC/katG (Line discontinued)
9145-I716362: Unmodified
9145-I716363: "Best Yield" (Mutant Line Discontinuted)
9145-I716364: Best All Around
9145-I716365: "Second Best All Around" (Mutant Line Discontinuted)

Biobricked petDUET Hemoglobin + SodC/KatG + Cytochrome b5/b5 reductase (Line discontinued)
9145-I716368: Unmodified cassette with antioxidants + cytochromes
9145-I716369: Best all around cassette with antioxidants + cytochromes

Biobricked petDUET Hemoglobin + sodC/katG + Cytochromes + AHSP(Line discontinued)
9145-I716370: Unmodified cassette
9145-I716371: Best all around cassette

Biobricked petDUET Hemoglobin + sodC/katG + Cytochromes + AHSP + metAP(Line discontinued)
9145-I716372: Unmodified cassette
9145-I716373: Best all around cassette

Biobricked petDUET Hemoglobin Cassettes + heme
9145-I716374: Unmodified cassette
9145-I716375: Best all around cassette

Biobricked petDUET Hemoglobin Cassettes + heme + Cytochromes
9145-I716376: Unmodified cassette
9145-I716377: Best all around cassette

Biobricked petDUET Hemoglobin Cassettes + heme + AHSP
9145-I716378: Unmodified cassette
9145-I716379: Best all around cassette

Biobricked petDUET Hemoglobin Cassettes + heme + sodC/katG
9145-I716380: Unmodified cassette
9145-I716381: Best all around cassette

Biobricked petDUET Hemoglobin + heme + cytochromes + sodC/katG
9145-I716383: Unmodified
9145-I716384: Best all around

Biobricked petDUET Hemoglobin + heme + cytochromes + sodC/katG + AHSP
9145-I716385: Unmodified
9145-I716386: Best all around

Biobricked petDUET Hemoglobin + heme + cytochromes + sodC/katG + AHSP + metAP
9145-I716386: Unmodified Final Construct
9145-I716387: Best all around Final Construct

Biobricked petDUET Hemoglobin + heme + sodC/katG + AHSP + metAP
9145-I716388: Unmodified
9145-I716389: Best all around

HemeABCD in pBACb
9145-I716382: pBACb with hemABCD

HemeABCD-TT in 9145
9145-I716390: HemABCD-TT in 9145

Unused Numbers

9145-I716391:

Samantha
Back to Notebook

Construction of pBca9125-I716201, I716202, I716203, I716204 (rbs+ATG variants)
Construction of pBca9125-I716205, I716206 (lox+Term variants)
Construction of pBca9125-I716207, I716208 (lox+Term+lox variants)
Construction of pBca9125-I716209 (ceaB biobrick)
Construction of pBca9125-I716210 (BamHI biobrick)
Construction of pBca9125-I716211 (Barnase biobrick)
Construction of pBca9125-I716212, I716213 (Cre biobricks with various start codons)
Construction of pBca9125-I716214, I716215 (rbs+ATG+Lox+Term+lox cassettes)
Construction of pBca9125-I716216, I716217 (cassettes+ceaB)
Construction of pBca9125-I716218, I716219 (cassettes+BamHI)
Construction of pBca9125-I716220, I716221 (cassettes+Barnase)
Construction of pBca9125-I716222, I716223 (cassettes+BglII)
Construction of pBca9125-I716224, I716225, I716226 (rbs library+Cre variants)
Construction of all [rbs][Cre][rbs][ATG][lox][term][lox][toxin] variants (I716227-I716250)
Construction of all [pBad][rbs][Cre][rbs][ATG][lox][term][lox][toxin] variants (I716401-I716415, plus I716416-I716421)
Construction of pBca9125-I716422, I716423 (cassettes+RFP)
Construction of pBca9125-I716424 through I716429 ([rbs][Cre][rbs][ATG][lox][term][lox][RFP] variants)
Construction of all [pBad][rbs][Cre][rbs][ATG][lox][term][lox][RFP] variants (I716430-I716435)
Construction of pBca1101-I716436 and pBca9125-I716437 (rbs+Cre variants)
Construction of pBca1101-I716438 and pBca9125-I716439 (rbs+Cre+TT variants)
Construction of pBca1101-I716440 (Cre+TTcassette+barnase)
Construction of pBca1101-I716441 (pbad.1106Arbs)
Construction of pBca1101-I716442 (pbad.1106Arbs.Cre.TTcassette.barnase)
Construction of pBca1101-I716443 and pBca9125-I716444 (rbs+Cre+TT+lox variants)
Construction of pBca1101-I716445 and pBca9125-I716446 (lox+rbs+Cre+TT+lox variants)
Construction of pBca1101-I716447 and pBca9125-I716448 (pbad+1090rbs+lox+rbs+Cre+TT+lox variants)
Construction of pBca9145-I716449 (pbad.1090rbs.ATG)
Construction of pBca9145-I716450 (pbad.1106Arbs.ATG)
Construction of pBca9125-I716451 through I716454 ([pbad][1090][ATG][toxin] variants)
Construction of pBca9125-I716455 through I716458 ([pbad][1106A][toxin] variants)

Vaibhavi
Biobrickification of composite part: Ptet + RFP (product = I716251)
Biobrickification of basic part in plasmid pBca9145-Bca1145 for the SodC ORF from Escherichia coli K-12 MG1655 (product = I716252)
Biobrickification of basic part in plasmid pBca9145-Bca1145 for the HPI, katG ORF from Salmonella typhimurium LT2 (product = I716253)
Biobrickification of basic part in plasmid pBca9145-Bca1145 for the map (methionine aminopeptidase) ORF from Escherichia coli K-12 MG1655 (product = I716254)
Biobrickification of composite part: RBS (pBca 9145 – Bca1090) + map gene (product = I716255)
Biobrickification of composite part: RBS (pBca 9145 – Bca1090) + AHSP gene gene (product = I716256)
Biobrickification of composite part: RBS (pBca 9145 – Bca1090) + sodC gene (product = I716257)
Biobrickification of composite part: RBS (pBca 9145 – Bca1090) + katG, HPI gene (intermediate product = I716258/I716259; final product = I716260)
Biobrickification of composite part: Composite part of RBS (pBca1101 – I716051) + map gene (product = I716261)
Biobrickification of composite part: RBS (pBca1101 – I716052) + AHSP gene (product = I716262)
Biobrickification of composite part: RBS (pBca1101 – I716051) + SodC gene (product = I716263)
Biobrickification of composite part: RBS (pBca1101 – I716052) + katG, HPI (product = I716264)
Biobrickification of composite part: [1090 rbs + katG gene (I716260)]+ [1090 rbs + sodC gene (I716265)] (product = I716265)
Biobrickification of composite part: 52 rbs library + katG gene (I716264)]+ [51 rbs library + sodC gene (I716263)] (product = I716266)

David
<< Back to David Tulga's Notebook

Basic Parts

pI716101 (Low Copy ampR Plasmid - Produces RFP)

pir I716102 (R6K Origin Inducer)

T7rnap I716103, I716104 (T7 RNA Polymerase)

T7 Promoters I716105, I716106, I716107

Composite Parts

I716108: RBS Library + pir

I716110,I716111: RBS Library + T7rnap ATG, GTG

Kristin
6/6/07 Construction of hemA basic part from R. capsulatus
6/6/07 Construction of hemB basic part from E.Coli K-12 MG1655
6/6/07 Construction of hemC basic part from E.Coli K-12 MG1655
6/6/07 Construction of hemD basic part from E.Coli K-12 MG1655
6/6/07 Construction of hemA basic part from E.Coli CFT073
6/15/07 Composite part of hemA from R.capsulatus and RBS pBca1101-I716051
6/15/07 Composite part of hemA from CFT073 and RBS pBca1101-I716051
6/15/07 Composite part of hemB from MG1655 and RBS pBca1101-I716052
6/15/07 Composite part of hemC from MG1655 and RBS pBca1101-I716051
6/15/07 Composite part of hemD from MG1655 and RBS pBca1101-I716052
6/26/07 Composite part of hemA from R.capsulatus and RBS pBca1101-1106A
6/26/07 Composite part of hemA from CFT073 and RBS pBca1101-1106A
6/26/07 Composite part of hemB from MG1655 and RBS pBca1101-1106A
6/26/07 Composite part of hemC from MG1655 and RBS pBca1101-1106A
6/26/07 Composite part of hemD from MG1655 and RBS pBca1101-1106A
7/9/07 Composite part of hemA from R.capsulatus + hemB
7/9/07 Composite part of hemA from CFT073+hemB
7/9/07 Composite part of hemC + hemD
7/9/07 Composite part of library RBS hemA from R.capsulatus + hemB
7/9/07 Composite part of library RBS hemA from CFT073 + hemB
7/9/07 Composite part of library RBS hemC + hemD
7/11/07 Composite part of library RBS hemA from R. capsulatus+hemB+hemC+hemD
7/11/07 Composite part of library RBS hemA from CFT073+hemB+hemC+hemD
7/17/07 Composite part of library RBS hemA from R.capsulatus/hemB/hemC/hemD+T7 wildtype promoter
7/17/07 Composite part of library RBS hemA from CFT073/hemB/hemC/hemD+T7 wildtype promoter
8/8/07 Composite part of hemA from R.capsulatus+hemB and hemD
8/8/07 Composite part of hemA from CFT073+hemB and hemD
8/8/07 Composite part of T7 wildtype promoter and library hemA from R.capsulatus
8/8/07 Composite part of T7 wildtype promoter and library hemA from CFT073
8/8/07 Composite part of T7+library hemA from R.capsulatus and library hemB
8/8/07 Composite part of T7+library hemA from CFT073 and library hemB

8/15/07 Composite part of T7+library hemA from R.capsulatus+library hemB and library hemC

Arthur
6/6 Bbrick ORF wbbL from pJ23006-Bca9106
6/6 Bbrick ORF neuS from pJ23006-Bca9106
6/8 Bbrick yfbE from MG1665
6/15 I716003a (pBca9145- cmr cass+rbs+neuS)
6/15 I716004 (pBca9145- yfbE_pro-rbs-RFP)
6/19 composite part <cm><rbs><neuS> (library)
6/19 composite part <kan><rbs><wbbL> (library)
6/26 I716008 (Ptet-rbs-wbbL-rbs-neuS)
6/27 I716009 cytB5+cytB5red
6/28 I716009 (cm+rbs+cytB5)
6/28 I716010 (kan+rbs+cytB5red)
7/2 I716011 cm-rbs-cytB5-rbs-cytB5red
7/2 I716012 ptet/rbs/wbbL/rbs/neuS in lo copy
7/3 yfbE try 2 I716013 I716014 I716015
7/10 I716013 (pBca9145-yfbE-rbs-ATG)
7/10 I716014 (pBca9145-yfbE_solo)
7/10 I716015 (pBca9145-RFP_noATG)
7/13 I716016 (yfbE-rbs-RFP_jp)
7/19 I716017 (yfbE-rbs-RFP)
7/16 I716018 (t7-cytb5-red)
7/17 I716019 (t7-cytb5-red-term)
7/19 I716020 (pBca1176) (CmR-colE1 on locopy)
7/19 I716021 (pSal-CmR-colE1 on locopy)
7/19 I716022 (p_yfbE-CmR-colE1 on locopy)
7/30 I716023 (ptet-rbs-wbbL-rbs-neuS)
7/31 I716024 (VHb from pRED2)
7/31 I716025 ((NcoI-EcoRI) VHb from pRED2)
7/31 I716026 ( p-zhuC)
7/31 I716027 (hemA+cytB5cassette)
7/31 I716028 I716029 (p-mgrB)

Rickey
Description of construction file here