Imperial/Wet Lab/DNA Constructs
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= Wet Lab: DNA Constructs = | = Wet Lab: DNA Constructs = | ||
==Constructs Overview== | ==Constructs Overview== | ||
Here are several tables listing the bricks which we are cloning, constructing and using, with their relevant details. | Here are several tables listing the bricks which we are cloning, constructing and using, with their relevant details. | ||
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===Cloning Table=== | ===Cloning Table=== | ||
- | Status of biobricks cloned and their applications: | + | Status of biobricks cloned and their applications:<br> |
+ | <font size="-2">Legend: I (Information), [Status: <font color=#CC0000>XL1</font> - cloned in XL1-Blue; <font color=#CC00FF>''Maxi''</font> - maxiprepped; <font color=#0000FF>''Midi''</font> - midiprepped; <font color=#00CC00>''Mini''</font> - miniprepped; <font color=#FF6633>BL21</font> - cloned in BL21(DE3); <small>status</small> - stocks running low]</font> | ||
{| style="width:95%; background:#33CCFF; border:1px solid #00CCFF" align="center" | {| style="width:95%; background:#33CCFF; border:1px solid #00CCFF" align="center" | ||
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
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<!-- PROMOTERS WITH GFP --> | <!-- PROMOTERS WITH GFP --> | ||
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || | + | || [[Imperial/Cell_by_Date/Testing|I]] || 02 || [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] || ptet-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font> || --- || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 1]] |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
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|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || | + | || [[Imperial/Infector_Detector/F2620_Comparison|I]] || 18 || [http://partsregistry.org/Part:BBa_T9002 BBa_T9002] || ptet-luxR-plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF><small>''Midi''</small></font>, <font color=#FF6633>BL21</font> || --- || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 1]] |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
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|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
|| || 25 || [http://partsregistry.org/Part:BBa_J37032 BBa_J37032] || plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF>''Midi''</font> || --- || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 2]] | || || 25 || [http://partsregistry.org/Part:BBa_J37032 BBa_J37032] || plux-GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF>''Midi''</font> || --- || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 2]] | ||
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<!-- BRICKS WITH PLASMID VECTORS --> | <!-- BRICKS WITH PLASMID VECTORS --> | ||
<!-- there are none of there : (--> | <!-- there are none of there : (--> | ||
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|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || || 23 || [http://partsregistry.org/Part:BBa_I13504 BBa_I13504] || GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF>''Midi''</font> || pT7 || | + | || || 23 || [http://partsregistry.org/Part:BBa_I13504 BBa_I13504] || GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#0000FF>''Midi''</font> || pT7 || Used to construct [http://partsregistry.org/Part:BBa_I719015 BBa_I719015] |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
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<!-- BRICKS BEING ORDERED --> | <!-- BRICKS BEING ORDERED --> | ||
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || || || BBa_I719??? || DsRed Express || | + | || || || BBa_I719??? || DsRed Express || ''Delayed'' || ptet, plux, pT7 || The Visual reporter |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || || || BBa_I719??? || HrpR-HrpS || | + | || || || BBa_I719??? || HrpR-HrpS || ''Ready'' || ??? || Hrp regulators |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || || || BBa_I719??? || pHrpL || | + | || || || BBa_I719??? || pHrpL || ''Ready'' || ??? || Hrp promoter |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
- | || || || BBa_I719??? || HrpV || | + | || || || BBa_I719??? || HrpV || ''Ready'' || ??? || Hrp inhibitor system |
|- style="background:#CCFFFF" align="center" | |- style="background:#CCFFFF" align="center" | ||
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===Ligation Table=== | ===Ligation Table=== | ||
- | Status of parts ligated and their applications: | + | Status of parts ligated and their applications:<br> |
+ | <font size="-2">Legend: I (Information), [Status: <font color=#CC0000>XL1</font> - cloned in XL1-Blue; <font color=#CC00FF>''Maxi''</font> - maxiprepped; <font color=#0000FF>''Midi''</font> - midiprepped; <font color=#00CC00>''Mini''</font> - miniprepped; <font color=#FF6633>BL21</font> - cloned in BL21(DE3); <small>status</small> - stocks running low]</font> | ||
{| style="width:95%; background:#00DD33; border:1px solid #00CC33" align="center" | {| style="width:95%; background:#00DD33; border:1px solid #00CC33" align="center" | ||
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|width="--"%|Application | |width="--"%|Application | ||
|- style="background:#CCFFCC" align="center" | |- style="background:#CCFFCC" align="center" | ||
- | || | + | || [[Imperial/Wet_Lab/Results/Res1.9|I]] || || [http://partsregistry.org/Part:BBa_I719015 BBa_I719015] || pT7 & GFP || <font color=#CC0000>XL1</font>, <font color=#CC00FF>''Maxi''</font>, <font color=#00CC00>''Mini''</font>, <font color=#FF6633>BL21</font> || pT7 + [http://partsregistry.org/Part:BBa_I13504 BBa_I13504] || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 2]] |
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|- style="background:#CCFFCC" align="center" | |- style="background:#CCFFCC" align="center" | ||
- | || || || BBa_I719??? || pT7 & DsRedEx || Planned || pT7 + DsRedEx || | + | || || || BBa_I719??? || pT7 & DsRedEx || Planned || pT7 + DsRedEx || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 2]] with visual reporter |
|- style="background:#CCFFCC" align="center" | |- style="background:#CCFFCC" align="center" | ||
- | || || || BBa_I719??? || ptet & DsRedEx || Planned || [http://partsregistry.org/Part:BBa_R0040 BBa_R0040] + DsRedEx || | + | || || || BBa_I719??? || ptet & DsRedEx || Planned || [http://partsregistry.org/Part:BBa_R0040 BBa_R0040] + DsRedEx || [[Imperial/Cell_by_Date/Design#DNA_Constructs|Cell By Date concept 1]] with visual reporter |
|- style="background:#CCFFCC" align="center" | |- style="background:#CCFFCC" align="center" | ||
- | || || || BBa_I719??? || ptet-luxR-plux-DsRedEx || Planned || [http://partsregistry.org/Part:BBa_T2620 BBa_F2620] + DsRedEx || | + | || || || BBa_I719??? || ptet-luxR-plux-DsRedEx || Planned || [http://partsregistry.org/Part:BBa_T2620 BBa_F2620] + DsRedEx || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 1]] with visual reporter |
|- style="background:#CCFFCC" align="center" | |- style="background:#CCFFCC" align="center" | ||
- | || || || BBa_I719??? || plux-DsRedEx || Planned || [http://partsregistry.org/Part:BBa_R0062 BBa_R0062] + DsRedEx || | + | || || || BBa_I719??? || plux-DsRedEx || Planned || [http://partsregistry.org/Part:BBa_R0062 BBa_R0062] + DsRedEx || [[Imperial/Infector_Detector/Design#DNA_Constructs|Infector Detector construct 2]] with visual reporter |
|- style="background:#CCFFCC" align="center" | |- style="background:#CCFFCC" align="center" | ||
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|} | |} | ||
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===Parts from the Registry=== | ===Parts from the Registry=== | ||
- | Physical information of biobricks: | + | Physical information of biobricks:<br> |
+ | <font size="-2">Legend: A (Available), W (Working) [<font color=#00CC00>W</font> - working ''in vivo'', <font color=#0000FF>W</font> - working ''in vitro'', <font color=#990033>X</font> - faulty], G (Checked on gel) [<font color=#339900>G</font> - incorrect size; <font color=#990033>X</font> - does not appear on gel], S (Sequenced) [<font color=#FF9900>S</font> - partially sequenced]</font> | ||
{| style="width:95%; background:#FF3399; border:1px solid #FF0099" align="center" | {| style="width:95%; background:#FF3399; border:1px solid #FF0099" align="center" | ||
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|width=7%| Conc. <br> (ng/ul) | |width=7%| Conc. <br> (ng/ul) | ||
|- style="background:#FFCCFF" align="center" | |- style="background:#FFCCFF" align="center" | ||
- | || A || <font color=#0000FF>W</font> || G || | + | || A || <font color=#0000FF>W</font> || G || S || 02 || [http://partsregistry.org/Part:BBa_I13522 BBa_I13522] || GFP under tetracyclin promoter || [http://partsregistry.org/Part:pSB1A2 pSB1A2] || AmpR || High || 937bp || 3016bp || Well 15H, Plate 2 || 500 |
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- | || A || W || G || | + | || A || W || G || S || 07 || [http://partsregistry.org/Part:BBa_F2620 BBa_F2620] || lux promoter, with luxR || [http://partsregistry.org/Part:pSB1A2 pSB1A2] || AmpR || High || 1061bp || 3140bp || Well 6B, Plate 1 || 80 |
|- style="background:#FFCCFF" align="center" | |- style="background:#FFCCFF" align="center" | ||
- | || A || <font color=#990033>X</font> || <font color=#339900>G</font> || | + | || A || <font color=#990033>X</font> || <font color=#339900>G</font> || S || 11 || [http://partsregistry.org/Part:BBa_E7104 BBa_E7104] || T7 GFP|| [http://partsregistry.org/Part:pSB1A2 pSB1A2] || AmpR || High || 826bp || 2905bp || Well 13F, Plate 2 || 100 |
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- | || A || <font color=#0000FF>W</font> || G || | + | || A || <font color=#0000FF>W</font> || G || <font color=#FF9900>S</font> || 18 || [http://partsregistry.org/Part:BBa_T9002 BBa_T9002] || GFP under lux promoter with LuxR || [http://partsregistry.org/Part:pSB1A3 pSB1A3] || AmpR || High || 1945bp || 4102bp || Well 19B, Plate 2 || 460 |
|- style="background:#FFCCFF" align="center" | |- style="background:#FFCCFF" align="center" | ||
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|- style="background:#FFCCFF" align="center" | |- style="background:#FFCCFF" align="center" | ||
- | || A || W || G || | + | || A || W || G || S || 23 || [http://partsregistry.org/Part:BBa_I13504 BBa_I13504] || GFP || [http://partsregistry.org/Part:pSB1A2 pSB1A2] || AmpR || High || 875bp || 2954bp || Well 16E, Plate 1 || 120/330 |
|- style="background:#FFCCFF" align="center" | |- style="background:#FFCCFF" align="center" | ||
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===Our Parts=== | ===Our Parts=== | ||
- | Physical information of our ligated parts: | + | Physical information of our ligated parts:<br> |
+ | <font size="-2">Legend: A (Available), W (Working) [<font color=#00CC00>W</font> - working ''in vivo'', <font color=#0000FF>W</font> - working ''in vitro'', <font color=#990033>X</font> - faulty], G (Checked on gel) [<font color=#339900>G</font> - incorrect size; <font color=#990033>X</font> - does not appear on gel], S (Sequenced)<br>Concentrations are given in ng/μl</font> | ||
{| style="width:95%; background:#FF9933; border:1px solid #FF6633" align="center" | {| style="width:95%; background:#FF9933; border:1px solid #FF6633" align="center" | ||
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|width=12%| Stock | |width=12%| Stock | ||
|- style="background:#FFFFBB" align="center" | |- style="background:#FFFFBB" align="center" | ||
- | || | + | || A || W || G || S || || [http://partsregistry.org/Part:BBa_I791005 BBa_I791005] || T7 promoter || pSB1A2 || AmpR || High || 23bp || 2102bp || |
|- style="background:#FFFFBB" align="center" | |- style="background:#FFFFBB" align="center" | ||
- | || | + | || A || <font color=#0000FF>W</font> || G || S || || [http://partsregistry.org/Part:BBa_I791015 BBa_I791015] || GFP under T7 promoter || pSB1A2 || AmpR || High || 906bp || 2985bp || |
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|- style="background:#FFFFBB" align="center" | |- style="background:#FFFFBB" align="center" | ||
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|} | |} | ||
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===Part Graveyard=== | ===Part Graveyard=== | ||
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|- style="background:#DDDDDD" align="center" | |- style="background:#DDDDDD" align="center" | ||
- | || A || || 26 || BBa_S03119 || ptet-LuxR || pSB1A2 || XL1, Midi | + | || A || || 26 || BBa_S03119 || ptet-LuxR || pSB1A2 || 998bp || XL1, Midi || not used in design |
|- style="background:#DDDDDD" align="center" | |- style="background:#DDDDDD" align="center" | ||
- | || A || || 27 || pSB1A3 || pSB1A3 || pSB1A3 || failed-XL1 | + | || A || || 27 || pSB1A3 || pSB1A3 || pSB1A3 || 2157bp || failed-XL1 || biobrick not present |
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|} | |} | ||
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+ | <center>| [[Imperial/Wet_Lab| Wet Lab >>]]</center> |
Latest revision as of 02:16, 27 October 2007
Wet Lab: DNA Constructs
Constructs Overview
Here are several tables listing the bricks which we are cloning, constructing and using, with their relevant details.
Cloning Table
Status of biobricks cloned and their applications:
Legend: I (Information), [Status: XL1 - cloned in XL1-Blue; Maxi - maxiprepped; Midi - midiprepped; Mini - miniprepped; BL21 - cloned in BL21(DE3); status - stocks running low]
I | ID | Part | Description | Status | Ligation Target | Use in Constructs |
I | 02 | BBa_I13522 | ptet-GFP | XL1, Maxi, Mini, BL21 | --- | Cell By Date concept 1 |
11 | BBa_E7104 | pT7 GFP | XL1, Maxi, Midi, Mini, BL21 | --- | Cell By Date concept 2 | |
30 | --- | pT7 (strong GFP) | XL1, Maxi, Mini, BL21 | --- | Construct to test T7 promoter | |
I | 18 | BBa_T9002 | ptet-luxR-plux-GFP | XL1, Maxi, Midi, BL21 | --- | Infector Detector construct 1 |
05 | BBa_R0040 | ptet | XL1, Midi, Mini | DsRedEx | Cell By Date concept 1 with visual reporter | |
BBa_I719005 | pT7 | Midi | DsRedEx | Cell By Date concept 2 | ||
07 | BBa_F2620 | ptet-luxR-plux | XL1, Midi, Mini | DsRedEx | Infector Detector construct 1 with visual reporter | |
21 | BBa_J23039 | ptet-luxI | XL1, Midi | --- | AHL sender construct | |
24 | BBa_R0062 | plux | XL1, Midi | DsRedEx | Infector Detector construct 2 with visual reporter | |
25 | BBa_J37032 | plux-GFP | XL1, Maxi, Midi | --- | Infector Detector construct 2 | |
13 | BBa_B0015 | Double terminator | XL1, Maxi, Midi, Mini | --- | General part construction | |
17 | BBa_I13507 | RFP | XL1, Midi | --- | Not being used anymore | |
19 | BBa_B0034 | strong RBS | XL1 | --- | General part construction | |
23 | BBa_I13504 | GFP | XL1, Maxi, Midi | pT7 | Used to construct BBa_I719015 | |
BBa_I719??? | DsRed Express | Delayed | ptet, plux, pT7 | The Visual reporter | ||
BBa_I719??? | HrpR-HrpS | Ready | ??? | Hrp regulators | ||
BBa_I719??? | pHrpL | Ready | ??? | Hrp promoter | ||
BBa_I719??? | HrpV | Ready | ??? | Hrp inhibitor system | ||
Ligation Table
Status of parts ligated and their applications:
Legend: I (Information), [Status: XL1 - cloned in XL1-Blue; Maxi - maxiprepped; Midi - midiprepped; Mini - miniprepped; BL21 - cloned in BL21(DE3); status - stocks running low]
I | ID | Part | Description | Status | Parents | Application |
I | BBa_I719015 | pT7 & GFP | XL1, Maxi, Mini, BL21 | pT7 + BBa_I13504 | Cell By Date concept 2 | |
BBa_I719??? | DsRedEx & pSB1A3 | Paused | DsRedEx + BBa_P1010 | Biobrick Submission | ||
BBa_I719??? | pT7 & DsRedEx | Planned | pT7 + DsRedEx | Cell By Date concept 2 with visual reporter | ||
BBa_I719??? | ptet & DsRedEx | Planned | BBa_R0040 + DsRedEx | Cell By Date concept 1 with visual reporter | ||
BBa_I719??? | ptet-luxR-plux-DsRedEx | Planned | BBa_F2620 + DsRedEx | Infector Detector construct 1 with visual reporter | ||
BBa_I719??? | plux-DsRedEx | Planned | BBa_R0062 + DsRedEx | Infector Detector construct 2 with visual reporter | ||
Parts from the Registry
Physical information of biobricks:
Legend: A (Available), W (Working) [W - working in vivo, W - working in vitro, X - faulty], G (Checked on gel) [G - incorrect size; X - does not appear on gel], S (Sequenced) [S - partially sequenced]
A | W | G | S | ID | Name | Description | Plasmid | Resist | Copy | Size(B) | Size(T) | Location | Conc. (ng/ul) |
A | W | G | S | 02 | BBa_I13522 | GFP under tetracyclin promoter | pSB1A2 | AmpR | High | 937bp | 3016bp | Well 15H, Plate 2 | 500 |
A | W | G | 05 | BBa_R0040 | tetracyclin promoter | pSB1A2 | AmpR | High | 54bp | 2133bp | Well 7O, Plate 1 | 60 | |
A | W | G | S | 07 | BBa_F2620 | lux promoter, with luxR | pSB1A2 | AmpR | High | 1061bp | 3140bp | Well 6B, Plate 1 | 80 |
A | X | G | S | 11 | BBa_E7104 | T7 GFP | pSB1A2 | AmpR | High | 826bp | 2905bp | Well 13F, Plate 2 | 100 |
A | W | G | 13 | BBa_B0015 | Double terminator | pSB1AK3 | A+KR | High | 129bp | 3316bp | Well 1B, Plate 2 | 100/70 | |
A | G | 17 | BBa_I13507 | RFP | pSB1A2 | AmpR | High | 861bp | 2940bp | Well 16N, Plate 1 | 80 | ||
A | W | G | S | 18 | BBa_T9002 | GFP under lux promoter with LuxR | pSB1A3 | AmpR | High | 1945bp | 4102bp | Well 19B, Plate 2 | 460 |
A | W | 19 | BBa_B0034 | RBS | pSB1A2 | AmpR | High | 12bp | 2091bp | Well 3O, Plate 1 | -- | ||
A | G | 21 | BBa_J23039 | Constitutive luxI | pSB1A2 | AmpR | High | 860bp | 2939bp | Well 11K, Plate 3 | 140 | ||
A | W | G | S | 23 | BBa_I13504 | GFP | pSB1A2 | AmpR | High | 875bp | 2954bp | Well 16E, Plate 1 | 120/330 |
A | G | 24 | BBa_R0062 | lux promoter | pSB1A2 | AmpR | High | 55bp | 2134bp | Well 9G, Plate 1 | 90 | ||
A | G | 25 | BBa_J37032 | GFP under lux promoter | pSB1A2 | AmpR | High | 938bp | 3017bp | Well 8D, Plate 3 | 125/330 | ||
W | 30 | --- | T7 with GFP(strong) | --- | Kan? | ??? | --- | ??? | --- | 150 | |||
Our Parts
Physical information of our ligated parts:
Legend: A (Available), W (Working) [W - working in vivo, W - working in vitro, X - faulty], G (Checked on gel) [G - incorrect size; X - does not appear on gel], S (Sequenced)
Concentrations are given in ng/μl
A | W | G | S | ID | Name | Description | Plasmid | Resist | Copy | Size(B) | Size(P) | Stock |
A | W | G | S | BBa_I791005 | T7 promoter | pSB1A2 | AmpR | High | 23bp | 2102bp | ||
A | W | G | S | BBa_I791015 | GFP under T7 promoter | pSB1A2 | AmpR | High | 906bp | 2985bp | ||
Part Graveyard
General information on parts we do not like...
A | W | ID | Name | Description | Plasmid | Size | Status | Notes |
A | W | 01 | BBa_E0040 | GFP | pSB1A2 | 720bp | XL1, Mini | Redundant |
A | 03 | BBa_J5528 | pBad-GFP | pSB2K3 | 2093bp | failed-XL1 | ara construct abandoned | |
A | 04 | BBa_J24677 | plux-GFP | pSB1A2 | 1787bp | XL1, Mini | Wrong GFP ligated | |
A | 06 | BBa_I0500 | pBad | pSB2K3 | 1210bp | XL1, Mini, Midi | ara construct abandoned | |
A | W | 08 | BBa_F1610 | luxI | pSB1AK3 | 798bp | XL1, Mini, Midi | Substitute part J23039 |
A | W | 09 | BBa_R0010 | lacI-plac | pSB1A2 | 200bp | XL1, Mini | Lac construct abandoned |
A | W | 10 | BBa_E1010 | RFP | pSB2K3 | 681bp | XL1, Mini | Substitute part I13507 |
A | 12 | BBa_S03550 | araC | pSB1AC3 | 958bp | XL1, Mini, Midi | araC construct abandoned | |
W | 14 | BBa_R0051 | pcI | pSB1A2 | 49bp | Biobrick | pcI construct abandoned | |
A | 15 | BBa_J07037 | cI-GFP | pSB2K3 | 912bp | XL1, Mini | No RBS present on this part | |
A | W | 16 | BBa_E0240 | GFP | pSB1A2 | 876bp | XL1, Midi | Redundant |
W | 20 | --- | AraC | pSB1AC3 | 1095bp | Planned | araC construct abandoned | |
A | 26 | BBa_S03119 | ptet-LuxR | pSB1A2 | 998bp | XL1, Midi | not used in design | |
A | 27 | pSB1A3 | pSB1A3 | pSB1A3 | 2157bp | failed-XL1 | biobrick not present | |
A | W | 28 | BBa_P1010 | pSB1A3 (ccd) | pSB1A3 | 0bp | failed-XL1 | Strain not available |
A | W | 29 | BBa_P1010 | pSB1A2 (ccd) | pSB1A2 | 0bp | --- | Strain not available |