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Richard Murray Lab: CIDAR MoClo Extension
Unpublished

Plasmids from Article

ID Plasmid Purpose  
120934P1mMoClo golden gate assembly AB part plasmid for J23101 (strength 1791x Anderson promoter; see http://parts.igem.org/Promoters/Catalog/Anderson); AB overhangs.
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120935p3mMoClo golden gate assembly AB part for J23150 (strength ~400x Anderson promoter; see http://parts.igem.org/Promoters/Catalog/Anderson) - Please see Supplemental Documents for annotated Genbank file
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120936p4mMoClo golden gate assembly AB part for J23151 (strength ~900x Anderson promoter; see http://parts.igem.org/Promoters/Catalog/Anderson) - Please see Supplemental Documents for annotated Genbank file
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120937P9mMoClo golden gate assembly AB part for pOR1-OR2 (lambda cI-repressable strong promoter) - Please see Supplemental Documents for annotated Genbank file
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120938P12mMoClo golden gate assembly AB part for pLas-TetO (Promoter activated by LasR and repressed by TetR; encodes <3OC12 AHL AND aTc> logic). Please see Supplemental Documents for annotated Genbank file.
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120939P15mMoClo golden gate assembly AB part for pCin-TetO (Promoter activated by CinR and repressed by TetR; encodes <3OC14 AHL AND aTc> logic). Please see Supplemental Documents for annotated Genbank file.
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120940P16mMoClo golden gate assembly AB part for pCin-LacO (Promoter activated by CinR and repressed by LacI; encodes <3OC14 AHL AND IPTG> logic). Please see Supplemental Documents for annotated Genbank file.
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120941P18mMoClo golden gate assembly AB part for T7 promoter (strong, T7 polymerase-dependent constitutive promoter; use with C95m). Please see Supplemental Documents for annotated Genbank file.
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120942P30mMoClo golden gate assembly AB part for pL-lacO1 (LacI-repressed promoter, as used in DOI:10.1038/35002125). Please see Supplemental Documents for annotated Genbank file.
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120943P32mMoClo golden gate assembly AB part for PlacO (common LacI-repressed promoter; see DOI: 10.1126/science.1256272). Please see Supplemental Documents for annotated Genbank file.
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120944P33mMoClo golden gate assembly AB part (medium-strength Mutalik library promoter; see DOI: 10.1038/nmeth.2404). Please see Supplemental Documents for annotated Genbank file.
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120945P34mMoClo golden gate assembly AB part (low-strength Mutalik library promoter; see DOI: 10.1038/nmeth.2404). Please see Supplemental Documents for annotated Genbank file.
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120946P35mMoClo golden gate assembly AB part for pLbda-CasRQi (strong lambda promoter with downstream dCas binding site for Qi-lab gRNA (UC16m); gRNA sequence taken from DOI: 10.1016/j.cell.2013.02.022).
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120947P37mMoClo golden gate assembly AB part for pRpa* (improved pRpa from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
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120948P38mMoClo golden gate assembly AB part for pTra* (improved pTra from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
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120949P57mMoClo golden gate assembly AB part for pCin* (Adam Meyer's improved pCin promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
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120950P58mMoClo golden gate assembly AB for pLas-A-10b (Adam Meyer's improved pLas promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
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120951P59mMoClo golden gate assembly AB part for pLux76B (Adam Meyer's improved pLux promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
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120952P60mMoClo golden gate assembly AB for pSalTTTC (Adam Meyer's improved pSal promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
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120953P61mMoClo golden gate assembly AB part for pTac (Adam Meyer's improved pTac promoter selected for dynamic range and low cross-sensitivity; unpublished, using strategy from https://doi.org/10.1101/285866).
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120954P66mMoClo golden gate assembly AB part for pRpa-AM (Adam Meyer's improved pRPA promoter from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
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120955C1mMoClo golden gate assembly CD part for deGFP (deGFP3 with 4aa N-truncation, 9aa C-truncation, F64L, and C203T (numbered with original sequence); see https://www.fpbase.org/protein/degfp3/)
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120956C3mMoClo golden gate assembly CD part for sfGFP (Superfolder green fluorescent protein from DOI: 10.1038/nbt1172; slight variant on https://www.fpbase.org/protein/superfolder-gfp/)
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120957C5mMoClo golden gate assembly CD part for mRFP (monomeric red fluorescent protein; see https://doi.org/10.1073/pnas.082243699 and https://www.fpbase.org/protein/mrfp1/).
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120958C9mMoClo golden gate assembly CD part for deCFP (cyan fluorescent protein) - Please see Supplemental Documents for annotated Genbank file
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120959C11mMoClo golden gate assembly CD part for Citrine (modified YFP; variant of https://www.fpbase.org/protein/citrine/) - Please see Supplemental Documents for annotated Genbank file
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120960C13mMoClo golden gate assembly CD part for Cerulean (modified CFP; variant of https://www.fpbase.org/protein/cerulean/) - Please see Supplemental Documents for annotated Genbank file
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120961C20mMoClo golden gate assembly CD part with sfYFP-ssrA (superfolder YFP with ssrA degradation tag; variant of https://www.fpbase.org/protein/yfp/)
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120962C21mMoClo golden gate assembly CD part for MG-aptamer (fluorescent RNA aptamer of malachite green; see DOI: 10.1021/ja0529788) - Please see Supplemental Documents for annotated Genbank file
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120963C22mMoClo golden gate assembly CD part for mSpinach (fluorescent RNA aptamer for DFHBI, suitable for in vivo use; see DOI: 10.1021/sb400089c). Please see Supplemental Documents for annotated Genbank file.
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120964C24mMoClo golden gate assembly CD part for lambda cI (repressor of pL or pOR1-OR2; use C64m for temperature-sensitive version). Please see Supplemental Documents for annotated Genbank file.
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120965C27mMoClo golden gate assembly CD part for TetR (tet repressor; identical to C2d but without ssrA degradation tag). Please see Supplemental Documents for annotated Genbank file.
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120966C31mMoClo golden gate assembly CD part for Bxb1 integrase. See DOI: 10.1007/s00438-006-0129-5. Please see Supplemental Documents for annotated Genbank file.
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120967C32mMoClo golden gate assembly CD part for CinR (Quorum-sensing receptor for 3OC14). Please see Supplemental Documents for annotated Genbank file.
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120968C33mMoClo golden gate assembly CD part for AiiA (AHL degradase; see doi: [10.1126/science.aaa3794]). Please see Supplemental Documents for annotated Genbank file.
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120969C35mMoClo golden gate assembly CD part for RhlR (Rhl quorum-sensing receptor for C4-HSL, synonymously modified to remove internal BbsI and BsaI cut sites).
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120970C36mMoClo golden gate assembly CD part for RhlI (quorum-sensing synthase for 3OC14). Please see Supplemental Documents for annotated Genbank file.
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120971C38mMoClo golden gate assembly CD for sigma38/RpoS (RNA polymerase active at transition from exponential phase to stationary phase). Please see Supplemental Documents for annotated Genbank file.
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120972C39mMoClo golden gate assembly CD part for ccdB (DNA gyrase toxin, modified synonymously to remove BsaI cut site; ccdA/C79m is antitoxin). Please see Supplemental Documents for annotated Genbank file.
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120973C40mMoClo golden gate assembly CD part for blank part (random 50bp sequence) - Please see Supplemental Documents for annotated Genbank file
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120974C41mMoClo golden gate assembly CD part for dCas9 (Catalytically-inactive S. pyogenes Cas9, for gRNA-targeted repression). Please see Supplemental Documents for annotated Genbank file.
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120975C51mMoClo golden gate assembly CD part for sfYFP (superfolder YFP; variant of https://www.fpbase.org/protein/yfp/ - Please see Supplemental Documents for annotated Genbank file
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120976C59mMoClo golden gate assembly CD part for mScarlet (RFP variant; see https://www.fpbase.org/protein/mscarlet/). Please see Supplemental Documents for annotated Genbank file.
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120977C61mMoClo golden gate assembly CD part for RpaR* (improved RpaR quorum-sensing activator from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
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120978C62mMoClo golden gate assembly CD part for TraR(W) (improved TraR quorum-sensing activator from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
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120979C63mMoClo golden gate assembly CD part for LacI (Lac repressor; identical to C1d but without ssrA degradation tag). Please see Supplemental Documents for annotated Genbank file.
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120980C64mMoClo golden gate assembly CD part for cI857 (temperature-sensitive lambda repressor that represses at 30C but not at 37C; see https://doi.org/10.1016/S0022-2836(66)80269-3. Use with P9m).
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120981C67mMoClo golden gate assembly CD part for Bxb1-mScarleti-LAA (Bxb1 integrase tagged with an mScarlet-I reporter and an LAA degradation tag). Please see Supplemental Documents for annotated Genbank file.
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120982C70mMoClo golden gate assembly CD part for RpaR-TYQEVV (Adam Meyer's improved RpaR activator selected for dynamic range and low cross-sensitivity using methods from https://doi.org/10.1101/285866,).
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120983C71mMoClo golden gate assembly CD part for CinR-CIDDHYRTC n-2 (Adam Meyer's improved CinR activator from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
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120984C72mMoClo golden gate assembly CD part for LacI-MVY (Adam Meyer's improved LacI repressor from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
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120985C73mMoClo golden gate assembly CD part for LasR-LSTPLVMI (Adam Meyer's improved LasR activator, selected for dynamic range and low cross-sensitivity with methods from https://doi.org/10.1101/285866).
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120986C74mMoClo golden gate assembly CD part for LuxRQ-FMY (Adam Meyer's improved LuxR activator from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
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120987C75mMoClo golden gate assembly CD part for NahRQ-VHAC (Adam Meyer's improved NahR activator from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
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120988C76mMoClo golden gate assembly CD part for KanR (kanamycin resistance protein). Please see Supplemental Documents for annotated Genbank file.
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120989C77mMoClo golden gate assembly CD partfor AmpR (ampicillin/carbenicillin resistance protein). Please see Supplemental Documents for annotated Genbank file.
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120990C78mMoClo golden gate assembly CD cloning part for ChlorR (chloramphenicol resistance protein). Please see Supplemental Documents for annotated Genbank file.
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120991C79mMoClo golden gate assembly CD part for ccdA (Antitoxin to ccdB/C39m. Sequence taken from pMAR7 plasmid sequence). Please see Supplemental Documents for annotated Genbank file.
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120992C80mMoClo golden gate assembly CD part for mfLon protease (see doi: [10.1038/nbt.3053]). Please see Supplemental Documents for annotated Genbank file.
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120993C82mMoClo golden gate assembly CD part for RpaI (synthase for Rpa-detected quorum sensing molecule 4-coumaroyl-homoserine lactone). Please see Supplemental Documents for annotated Genbank file.
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120994C83mMoClo golden gate assembly CD part for pir (Initiation factor required for replication of R6K origin plasmids). Please see Supplemental Documents for annotated Genbank file.
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120995C84mMoClo golden gate assembly CD part for sigma28/RpoF (RNA polymerase required for flagellar formation in E. coli). Please see Supplemental Documents for annotated Genbank file.
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120996C85mMoClo golden gate assembly CD part for sigmaX (Bacillus subtilis RNA polymerase involved in heat response and biofilm formation). Please see Supplemental Documents for annotated Genbank file.
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120997C86mMoClo golden gate assembly CD part (phage lysis protein; lethal to host when expressed). Please see Supplemental Documents for annotated Genbank file.
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120998C90mMoClo golden gate assembly CD part for NahR-sfGFP fusion (Adam Meyer improved NahR (C75m) fused to superfolder GFP (C3m)). Please see Supplemental Documents for annotated Genbank file.
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120999C91mMoClo golden gate assembly CD part for sfCFP (superfolder CFP developed by Ye Chen in Matthew Bennet's lab) - Please see Supplemental Documents for annotated Genbank file
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121000C92mMoClo golden gate assembly CD part for sfCFP-pdt3 (superfolder CFP developed by Ye Chen in Matthew Bennet's lab, with a pdt3 tag for mfLon protease).
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121001C95mMoClo golden gate assembly CD part for T7 RNA polymerase (use with P18m). Please see Supplemental Documents for annotated Genbank file.
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121002C98mMoClo golden gate assembly CD part for Gp2 (RNA polymerase inhibitor from T7 phage; lethal to host when expressed). Please see Supplemental Documents for annotated Genbank file.
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121003C99mMoClo golden gate assembly CD part for codon-optimized mScarlet-I (fast-folding mScarlet variant, codon-optimized for E. coli; see https://www.fpbase.org/protein/mscarlet-i/).
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121004C100mMoClo golden gate assembly CD part sfYFP-ptd3 (superfolder YFP with pdt3 degradation tag for mfLon). Please see Supplemental Documents for annotated Genbank file.
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121005C101mMoClo golden gate assembly CD part sfCFP-LAA (superfolder CFP developed by Ye Chen in Matthew Bennet's lab, with LAA degradation tag for ssrA).
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121006C102mMoClo golden gate assembly CD part treRT-LAA (synthetic Lac-family repressor chimera with LAA degradation tag for ssrA; see DOI: 10.1021/sb500262f).
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121007C103mMoClo golden gate assembly CD part for mScarlet-I-LAA (fast-folding mScarlet variant, codon-optimized for E. col, with LAA degradation tag; see https://www.fpbase.org/protein/mscarlet-i/).
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121008C105mMoClo golden gate assembly CD part for sfYFP-AAV (superfolder YFP with AAV degradation tag for ssrA). Please see Supplemental Documents for annotated Genbank file.
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121009C106mMoClo golden gate assembly CD part for sfYFP-DAS (superfolder YFP with DAS degradation tag for ssrA). Please see Supplemental Documents for annotated Genbank file.
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121010C108mMoClo golden gate assembly CD part for mScarlet-I-pdt3 (fast-folding mScarlet variant, codon-optimized for E. col, with pdt3 degradation tag; see https://www.fpbase.org/protein/mscarlet-i/).
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121011C109mMoClo golden gate assembly CD part for mfLon-pdt3 (mfLon protease with self-targeting degradation tag pdt3). Please see Supplemental Documents for annotated Genbank file.
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121012C113mMoClo golden gate assembly CD part for Cas9 (S. pyogenes gRNA-targeted endonuclease Cas9). Please see Supplemental Documents for annotated Genbank file.
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121013C114mMoClo golden gate assembly CD part for Cas9 (S. pyogenes gRNA-targeted endonuclease Cas9, with bbsI cut sites removed synonymously). Please see Supplemental Documents for annotated Genbank file.
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121014C115mMoClo golden gate assembly CD part for TP901 integrase (Integrase from lactococcal phage TP901). Please see Supplemental Documents for annotated Genbank file.
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121015U2mMoClo golden gate assembly BC part for BCD11 (Medium-high expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121016U3mMoClo golden gate assembly BC part for BCD13 (Medium expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121017U4mMoClo golden gate assembly BC part for UTR1 (very strong RBS). Please see Supplemental Documents for annotated Genbank file.
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121018U5mMoClo golden gate assembly BC part for BCD14 (Medium expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121019U6mMoClo golden gate assembly BC part for BCD20 (Medium expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121020U7mMoClo golden gate assembly BC part for BCD16 (low expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121021U8mMoClo golden gate assembly BC part for BCD24 (low expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121022U9mMoClo golden gate assembly BC part for BCD22 (very low expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121023U17mMoClo golden gate assembly BC part for Bujard RBS (strong RBS from https://doi.org/10.1093/nar/25.6.1203). Please see Supplemental Documents for annotated Genbank file.
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121024U19mMoClo golden gate assembly BC part for MG-aptamer (fluorescent RNA aptamer of malachite green; see DOI: 10.1021/ja0529788) - Please see Supplemental Documents for annotated Genbank file
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121025U22mMoClo golden gate assembly BC part (high expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
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121026U24mMoClo golden gate assembly BC part for RiboJ-BCD2 (low expression bi-cistronic RBS, engineered for context-independence, prefixed by self-cleaving RiboJ; see https://doi.org/10.1038/nmeth.2404).
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121027U25mMoClo golden gate assembly BC part for RiboJ-UTR1 (very strong RBS, prefixed by self-cleaving RiboJ for upstream context independence). Please see Supplemental Documents for annotated Genbank file.
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121028T1mMoClo golden gate assembly DE part for T500 terminator Engineered terminator derived from bacteriophage 83; see DOI: 10.1126/science.284.5414.611).
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121029T2mMoClo golden gate assembly DE part for Eck120033736 (164.6x-strength natural terminator; see DOI: 10.1038/nmeth.2515) - Please see Supplemental Documents for annotated Genbank file
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121030T7mMoClo golden gate assembly DE part for tracrRNA terminator (natural terminator from S. pyogenes CRISPR-system tracrRNA). Please see Supplemental Documents for annotated Genbank file.
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121031T12mMoClo golden gate assembly DE part ECK120029600 (378x-strength natural terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
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121032T13mMoClo golden gate assembly DE part for ECK120033737 (313x-strength natural terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
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121033T14mMoClo golden gate assembly DE part for L3S1P13 (178x-strength synthetic terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
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121034T15mMoClo golden gate assembly DE part for L3S3P11 (173x-strength synthetic terminator, modified to remove BsaI cut site; see DOI: 10.1038/nmeth.2515).
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121035T16mMoClo golden gate assembly DE part for L3S2P55 (256x-strength synthetic terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
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121036T17mMoClo golden gate assembly DE part L3S2P11 (262x-strength synthetic terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
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121037T18mMoClo golden gate assembly DE part for L3S2P21 (382x-strength synthetic terminator with BsaI cut site removed; see DOI: 10.1038/nmeth.2515).
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121038UC16mMoClo golden gate assembly DE part for gQi gRNA (guide RNA for S. pyogenes Cas9; sequence from DOI: 10.1016/j.cell.2013.02.022). Please see Supplemental Documents for annotated Genbank file.
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121039UC17mMoClo golden gate assembly DE part for gV1 gRNA (guide RNA for S. pyogenes Cas9; sequence from doi: [10.15252/msb.20145735]). Please see Supplemental Documents for annotated Genbank file.
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121040UC20mMoClo golden gate assembly DE part for gN2 gRNA (guide RNA for S. pyogenes Cas9; sequence designed with NUPACK for stable tracrRNA structure and open targeting region).
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121041UCT1mMoClo golden gate assembly DE part for gQi gRNA (guide RNA for S. pyogenes Cas9; sequence from DOI: 10.1016/j.cell.2013.02.022). Please see Supplemental Documents for annotated Genbank file.
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121042V35mMoClo golden gate assembly AE destination vector DVCK-AE-GFP (ColE1/kan resistance destination vector with constitutive GFP expression for screening.
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121043V37mMoClo golden gate assembly AE destination vector DVCK-AE-mScar (ColE1/kan resistance destination vector with constitutive mScarlet expressing for screening.
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