Team:Heidelberg/Parts

From 2010.igem.org

(Difference between revisions)
(→Binding Site Patterns)
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== Basic parts ==
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==miTuning & miMeasure==
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<center>
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{| class="wikitable sortable" border="0" style="text-align: left"
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|-bgcolor=#cccccc
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|+ align="top, left"|
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|width=40px| ID||width=600px|Content||width=100px|Registry link||width=100px|Name
 +
|-
 +
|K3||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337036 BBa_K337036]|| pSMB_miTuner Plasmid HD3
 +
|-
 +
|K4||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337038 BBa_K337038]|| pSMB_miTuner Plasmid HD4
 +
|-
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|miM||sv40ter(rc)/eBFP(rc)/biCMV/eGFP(fw)/sv40ter(fw)||[http://partsregistry.org/Part:BBa_K337049 BBa_K337049]|| pSMB_miMeasure
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|-
 +
|}
 +
</center>
 +
 
 +
 
 +
==miTuning & miMeasure==
 +
<center>
 +
{| class="wikitable sortable" border="0" style="text-align: left"
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|-bgcolor=#cccccc
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|+ align="top, left"|(Physical DNA not submitted)
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|width=60px| Design||width=300px|Content||width=100px|Registry link||width=100px|Name
 +
|-
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|KD:97%||perfect binding site||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337052 BBa_K337052]||shRNA miRhaat
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|-
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|KD:69%||imperfect binding site: point mut 11||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337053 BBa_K337053]||shRNA miRhaat
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|-
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|KD:28%||imperfect binding site: bulge 16-18||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337054 BBa_K337054]||shRNA miRhaat
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|-
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|KD:96%||perfect binding site||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337055 BBa_K337055]||miR122
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|-
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|KD:64%||imperfect binding site:||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337056 BBa_K337056]||miR122
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|-
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|KD:24%||imperfect binding site:||[http://partsregistry.org/wiki/index.php?title=Part:BBa_K337057 BBa_K337057]||miR122
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|-
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|}
 +
</center>
 +
 
 +
 
 +
==Synthetic MicroRNA Binding Site Patterns==
 +
<center>
 +
{| class="wikitable sortable" border="0" style="text-align: left"
 +
|-bgcolor=#cccccc
 +
|+ align="top, left"|
 +
|width=40px|  ID||width=350px|Content||width=100px|Registry link
 +
|-
 +
|1.3||hsa-miR-122 Binding site pattern (3BS)||[http://partsregistry.org/Part:BBa_K337000 BBa_K337000]
 +
|-
 +
|1A||hsa-miR-122 Binding site pattern (4BS)||[http://partsregistry.org/Part:BBa_K337003 BBa_K337003]
 +
|-
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|1-5||hsa-miR-122 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337004 BBa_K337004]
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|-
 +
|3.7||hsa-miR-122 Binding site pattern (2BS - additional 10bp Spacer)||[http://partsregistry.org/Part:BBa_K337005 BBa_K337005]
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|-
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|1.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337006 BBa_K337006]
 +
|-
 +
|1.8||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337007 BBa_K337007]
 +
|-
 +
|3.1||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337008 BBa_K337008]
 +
|-
 +
|4.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337009 BBa_K337009]
 +
|-
 +
|4.6||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337010 BBa_K337010]
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|-
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|mir221-10L2||hsa-miR-221 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337011 BBa_K337011]
 +
|-
 +
|}
 +
</center>
 +
 
 +
 
 +
==Tunig Kit - Basic Parts==
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
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|+ align="top, left"|'''Table 1''': Our miBricks. Listed ID refers to internal nomenclature.
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|+ align="top, left"|
|width=40px|  ID||width=100px|Content||width=100px|Registry link|| width=300px|Comment
|width=40px|  ID||width=100px|Content||width=100px|Registry link|| width=300px|Comment
|-
|-
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</center>
</center>
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== Composite Parts ==
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==Tuning Kit -  Intermediate Parts 1==
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
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|+ align="top, left"|'''Table 2''': Our composite parts from subsequent assembling steps. Listed ID refers to internal nomenclature.
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|+ align="top, left"|
|width=40px|  ID||width=300px|Content||width=100px|Registry link||width=450px|Purpose of the cassette  
|width=40px|  ID||width=300px|Content||width=100px|Registry link||width=450px|Purpose of the cassette  
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|-
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</center>
</center>
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== Final Constructs ==
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==Tuning Kit -  Intermediate Parts 2==
<center>
<center>
{| class="wikitable sortable" border="0" style="text-align: left"
{| class="wikitable sortable" border="0" style="text-align: left"
|-bgcolor=#cccccc
|-bgcolor=#cccccc
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|+ align="top, left"|'''Table 3''': Our final constructs. Listed ID refers to internal nomenclature.
+
|+ align="top, left"|
|width=40px|  ID||width=600px|Content||width=100px|Registry link||width=100px|Name  
|width=40px|  ID||width=600px|Content||width=100px|Registry link||width=100px|Name  
|-
|-
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|K2||BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337035 BBa_K337035]|| pSMB_miTuner Plasmid HD2  
|K2||BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337035 BBa_K337035]|| pSMB_miTuner Plasmid HD2  
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|-
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|K3||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337036 BBa_K337036]|| pSMB_miTuner Plasmid HD3
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|-
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|K4||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/CMV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337038 BBa_K337038]|| pSMB_miTuner Plasmid HD4
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|-
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|K5||BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337040 BBa_K337040]|| pSMB_miTuner Plasmid HD5  
|K5||BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337040 BBa_K337040]|| pSMB_miTuner Plasmid HD5  
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|-
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|K8||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337046 BBa_K337046]|| pSMB_miTuner Plasmid HD8  
|K8||BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/RSV/Kozag_hRluc_BGH||[http://partsregistry.org/Part:BBa_K337046 BBa_K337046]|| pSMB_miTuner Plasmid HD8  
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|-
 
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|miM||sv40ter(rc)/eBFP(rc)/biCMV/eGFP(fw)/sv40ter(fw)||[http://partsregistry.org/Part:BBa_K337049 BBa_K337049]|| pSMB_miMeasure
 
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|-
 
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|}
 
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</center>
 
-
 
-
== Binding Site Patterns ==
 
-
<center>
 
-
{| class="wikitable sortable" border="0" style="text-align: left"
 
-
|-bgcolor=#cccccc
 
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|+ align="top, left"|'''Table 4''': Binding site patterns generated by miraPCR.
 
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|width=40px|  ID||width=350px|Content||width=100px|Registry link
 
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|-
 
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|1.3||hsa-miR-122 Binding site pattern (3BS)||[http://partsregistry.org/Part:BBa_K337000 BBa_K337000]
 
-
|-
 
-
|1A||hsa-miR-122 Binding site pattern (4BS)||[http://partsregistry.org/Part:BBa_K337003 BBa_K337003]
 
-
|-
 
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|1-5||hsa-miR-122 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337004 BBa_K337004]
 
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|-
 
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|3.7||hsa-miR-122 Binding site pattern (2BS - additional 10bp Spacer)||[http://partsregistry.org/Part:BBa_K337005 BBa_K337005]
 
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|-
 
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|1.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337006 BBa_K337006]
 
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|-
 
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|1.8||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337007 BBa_K337007]
 
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|-
 
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|3.1||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337008 BBa_K337008]
 
-
|-
 
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|4.5||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337009 BBa_K337009]
 
-
|-
 
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|4.6||hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12||[http://partsregistry.org/Part:BBa_K337010 BBa_K337010]
 
-
|-
 
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|mir221-10L2||hsa-miR-221 Binding site pattern (2BS)||[http://partsregistry.org/Part:BBa_K337011 BBa_K337011]
 
|-
|-
|}
|}

Revision as of 10:52, 27 October 2010

Parts

We assembled a lot of miBricks (i. e. basic parts) to composite parts that were then used to built up our final constructs. The submitted parts are listed below. We did not categorize the parts according to different subprojects since they are universally applicable or clearly denoted through their names. Some binding site patterns, which were created via [... miraPCR], are listed separately.


miTuning & miMeasure

IDContentRegistry linkName
K3BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337036 pSMB_miTuner Plasmid HD3
K4BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337038 pSMB_miTuner Plasmid HD4
miMsv40ter(rc)/eBFP(rc)/biCMV/eGFP(fw)/sv40ter(fw)BBa_K337049 pSMB_miMeasure


miTuning & miMeasure

(Physical DNA not submitted)
DesignContentRegistry linkName
KD:97%perfect binding siteBBa_K337052shRNA miRhaat
KD:69%imperfect binding site: point mut 11BBa_K337053shRNA miRhaat
KD:28%imperfect binding site: bulge 16-18BBa_K337054shRNA miRhaat
KD:96%perfect binding siteBBa_K337055miR122
KD:64%imperfect binding site:BBa_K337056miR122
KD:24%imperfect binding site:BBa_K337057miR122


Synthetic MicroRNA Binding Site Patterns

IDContentRegistry link
1.3hsa-miR-122 Binding site pattern (3BS)BBa_K337000
1Ahsa-miR-122 Binding site pattern (4BS)BBa_K337003
1-5hsa-miR-122 Binding site pattern (2BS)BBa_K337004
3.7hsa-miR-122 Binding site pattern (2BS - additional 10bp Spacer)BBa_K337005
1.5hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337006
1.8hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337007
3.1hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337008
4.5hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337009
4.6hsa-miR-122 Binding site pattern (2BS) with randomized nt9-12BBa_K337010
mir221-10L2hsa-miR-221 Binding site pattern (2BS)BBa_K337011


Tunig Kit - Basic Parts

IDContentRegistry linkComment
F1RSV fwBBa_K337012-
F2SV40 rcBBa_K337013-
F3RSV rcBBa_K337014-
F4BGH fwBBa_K337001-
F5BGH rcBBa_K337002 leads to insertion of BamHI site
F7microRNA 10HDBBa_K337016 template for creation of shRNA-like miRNA
F8CMV fwBBa_K337018-
F9FRT siteBBa_K337019-
F10hRlucBBa_K337025-
F16TetRBBa_K337028-
F17Luc2BBa_K337030 compatible for insertion of microRNA binding sites
biCMVbiCMVBBa_K337017-


Tuning Kit - Intermediate Parts 1

IDContentRegistry linkPurpose of the cassette
F6luc2_sv40terBBa_K337015 Luc2 reporter gene with terminator referring to SV40 promoter
F15CMV_TetO2BBa_K337027 CMV promoter under control of Tet Operator for regulation of gene expression
R1Sv40(rc)/RSV(fw)BBa_K337045 bidirectional hybrid promoter
R2Sv40(rc)/CMV(fw)BBa_K337047
R3RSV(rc)/CMV(fw)BBa_K337048
R4RSV(rc)/CMV_TetO2(fw)BBa_K337050
R5BGH(rc)/shRNA10(rc)BBa_K337051 synthetic microRNA template part
R13BGH(rc)/shRNA10(rc)/sv40(rc)/RSV(fw)BBa_K337020tuning construct cloning into reporter plasmid backbone containing a binding site against synthetic shRNA-like miRNA
R14BGH(rc)/shRNA10(rc)/sv40(rc)/CMV(fw)BBa_K337021
R15BGH(rc)/shRNA10(rc)/RSV(rc)/CMV(fw)BBa_K337022
R16BGH(rc)/shRNA10(rc)/RSV(rc)/CMV(fw)_TetO2(fw)BBa_K337023
R17BGH(rc)/shRNA6(rc)/sv40(rc)/RSV(fw)BBa_K337024
R18BGH(rc)/shRNA6(rc)/sv40(rc)/CMV(fw)BBa_K337026
R19BGH(rc)/shRNA6(rc)/RSV(rc)/CMV(fw)BBa_K337029
R20BGH(rc)/shRNA6(rc)/RSV(rc)/CMV_TetO2(fw)BBa_K337031tuning construct core containing Tet Operator for On-Targeting together with repressor construct
R21Luc2(rc)_sv40(rc)/CMV(fw)BBa_K337033 bidirectional hybrid promoter with Luc2 reference gene under control of SV40 promoter
R22Luc2(rc)_sv40(rc)/RSV(fw)BBa_K337034
R32Kozag_hRluc/BGH(fw)BBa_K337037reference reporter
R33TetR_mut(XhoI/XbaI)BBa_K337039mutagenized TetR including cutting sites to paste miRNA binding sites
T1BGH(rc)_CMV/TetR/BGH(fw)/BGH(rc)BBa_K337041repressor construct for On-Targeting together with tuning construct
T2BGH(rc)_RSV/TetR/BGH(fw)/BGH(rc)BBa_K337043


Tuning Kit - Intermediate Parts 2

IDContentRegistry linkName
K1BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337032 pSMB_miTuner Plasmid HD1
K2BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/Luc2_sv40/CMV/Kozag_hRluc_BGHBBa_K337035 pSMB_miTuner Plasmid HD2
K5BGH(rc)/shRNA10(rc)/sv40(rc)/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337040 pSMB_miTuner Plasmid HD5
K6BGH(rc)/shRNA10(rc)/sv40(rc)/CMV/RSV/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337042 pSMB_miTuner Plasmid HD6
K7BGH(rc)/shRNA10(rc)/RSV(rc)/CMV/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337044 pSMB_miTuner Plasmid HD7
K8BGH(rc)/shRNA10(rc)/RSV(rc)/CMV_TetO2/Luc2_sv40/RSV/Kozag_hRluc_BGHBBa_K337046 pSMB_miTuner Plasmid HD8


Retrieved from "http://2010.igem.org/Team:Heidelberg/Parts"