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< Imperial | Wet Lab(Difference between revisions)

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	[http://partsregistry.org/Part:BBa_I13522 BBa_I13522]	ptet-GFP	XL1, Maxi, Mini, BL21	---	Cell By Date concept 1
	11	[http://partsregistry.org/Part:BBa_E7104 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	[http://partsregistry.org/Part:BBa_T9002 BBa_T9002]	ptet-luxR-plux-GFP	XL1, Maxi, Midi, BL21	---	Infector Detector construct 1

	05	[http://partsregistry.org/Part:BBa_R0040 BBa_R0040]	ptet	XL1, Midi, Mini	DsRedEx	Cell By Date concept 1 with visual reporter
		[http://partsregistry.org/Part:BBa_I719005 BBa_I719005]	pT7	Midi	DsRedEx	Cell By Date concept 2
	07	[http://partsregistry.org/Part:BBa_F2620 BBa_F2620]	ptet-luxR-plux	XL1, Midi, Mini	DsRedEx	Infector Detector construct 1 with visual reporter

	21	[http://partsregistry.org/Part:BBa_J23039 BBa_J23039]	ptet-luxI	XL1, Midi	---	AHL sender construct
	24	[http://partsregistry.org/Part:BBa_R0062 BBa_R0062]	plux	XL1, Midi	DsRedEx	Infector Detector construct 2 with visual reporter
	25	[http://partsregistry.org/Part:BBa_J37032 BBa_J37032]	plux-GFP	XL1, Maxi, Midi	---	Infector Detector construct 2

	13	[http://partsregistry.org/Part:BBa_B0015 BBa_B0015]	Double terminator	XL1, Maxi, Midi, Mini	---	General part construction
	17	[http://partsregistry.org/Part:BBa_I13507 BBa_I13507]	RFP	XL1, Midi	---	Not being used anymore
	19	[http://partsregistry.org/Part:BBa_B0034 BBa_B0034]	strong RBS	XL1	---	General part construction
	23	[http://partsregistry.org/Part:BBa_I13504 BBa_I13504]	GFP	XL1, Maxi, Midi	pT7	Used to construct [http://partsregistry.org/Part:BBa_I719015 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		[http://partsregistry.org/Part:BBa_I719015 BBa_I719015]	pT7 & GFP	XL1, Maxi, Mini, BL21	pT7 + [http://partsregistry.org/Part:BBa_I13504 BBa_I13504]	Cell By Date concept 2

		BBa_I719???	DsRedEx & pSB1A3	Paused	DsRedEx + [http://partsregistry.org/Part:BBa_P1010 BBa_P1010]	Biobrick Submission

		BBa_I719???	pT7 & DsRedEx	Planned	pT7 + DsRedEx	Cell By Date concept 2 with visual reporter
		BBa_I719???	ptet & DsRedEx	Planned	[http://partsregistry.org/Part:BBa_R0040 BBa_R0040] + DsRedEx	Cell By Date concept 1 with visual reporter
		BBa_I719???	ptet-luxR-plux-DsRedEx	Planned	[http://partsregistry.org/Part:BBa_T2620 BBa_F2620] + DsRedEx	Infector Detector construct 1 with visual reporter
		BBa_I719???	plux-DsRedEx	Planned	[http://partsregistry.org/Part:BBa_R0062 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

[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

A

W

G

05

[http://partsregistry.org/Part:BBa_R0040 BBa_R0040]

tetracyclin promoter

[http://partsregistry.org/Part:pSB1A2 pSB1A2]

AmpR

High

54bp

2133bp

Well 7O, Plate 1

60

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

A

X

G

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

A

W

G

13

[http://partsregistry.org/Part:BBa_B0015 BBa_B0015]

Double terminator

[http://partsregistry.org/Part:pSB1AK3 pSB1AK3]

A+KR

High

129bp

3316bp

Well 1B, Plate 2

100/70

A

G

17

[http://partsregistry.org/Part:BBa_I13507 BBa_I13507]

RFP

[http://partsregistry.org/Part:pSB1A2 pSB1A2]

AmpR

High

861bp

2940bp

Well 16N, Plate 1

80

A

W

G

S

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

A

W

19

[http://partsregistry.org/Part:BBa_B0034 BBa_B0034]

RBS

[http://partsregistry.org/Part:pSB1A2 pSB1A2]

AmpR

High

12bp

2091bp

Well 3O, Plate 1

--

A

G

21

[http://partsregistry.org/Part:BBa_J23039 BBa_J23039]

Constitutive luxI

[http://partsregistry.org/Part:pSB1A2 pSB1A2]

AmpR

High

860bp

2939bp

Well 11K, Plate 3

140

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

A

G

24

[http://partsregistry.org/Part:BBa_R0062 BBa_R0062]

lux promoter

[http://partsregistry.org/Part:pSB1A2 pSB1A2]

AmpR

High

55bp

2134bp

Well 9G, Plate 1

90

A

G

25

[http://partsregistry.org/Part:BBa_J37032 BBa_J37032]

GFP under lux promoter

[http://partsregistry.org/Part:pSB1A2 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

[http://partsregistry.org/Part:BBa_I791005 BBa_I791005]

T7 promoter

pSB1A2

AmpR

High

23bp

2102bp

A

W

G

S

[http://partsregistry.org/Part:BBa_I791015 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

| Wet Lab >>

@@ Line 1: / Line 1: @@
 {{Template: IC07navmenu}}
 __NOTOC__
+<br clear="all">
 = 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:
+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="background:#CCFFFF" align="center"
@@ Line 21: / Line 21: @@
 <!-- PROMOTERS WITH GFP -->
 |- style="background:#CCFFFF" align="center"
-||  || 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]]
+|| [[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"
@@ Line 30: / Line 30: @@
 |- style="background:#CCFFFF" align="center"
-||  || 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]]
+|| [[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"
@@ Line 94: / Line 94: @@
 ===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="background:#CCFFCC" align="center"
@@ Line 105: / Line 106: @@
 |width="--"%|Application
 |- style="background:#CCFFCC" align="center"
-||  ||  || [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]]
+|| [[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]]
 |- style="background:#CCFFCC" align="center"
@@ Line 131: / Line 132: @@
 ||  ||  ||  ||  ||  ||  ||
 |}
-<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>
 ===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="background:#FFCCFF" align="center"
@@ Line 154: / Line 153: @@
 |width=7%| Conc. <br> (ng/ul)
 |- style="background:#FFCCFF" align="center"
-|| A || <font color=#0000FF>W</font> || G ||  || 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
+|| 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
 |- style="background:#FFCCFF" align="center"
@@ Line 160: / Line 159: @@
 |- style="background:#FFCCFF" align="center"
-|| A || W || G ||  || 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
+|| 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"
-|| A || <font color=#990033>X</font> || <font color=#339900>G</font> ||  || 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
+|| 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
 |- style="background:#FFCCFF" align="center"
@@ Line 172: / Line 171: @@
 |- style="background:#FFCCFF" align="center"
-|| A || <font color=#0000FF>W</font> || G ||  || 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
+|| 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"
@@ Line 181: / Line 180: @@
 |- style="background:#FFCCFF" align="center"
-|| A || W || G ||  || 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
+|| 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"
@@ Line 198: / Line 197: @@
 ===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="background:#FFFFBB" align="center"
@@ Line 215: / Line 215: @@
 |width=12%| Stock
 |- style="background:#FFFFBB" align="center"
-||  ||  ||  ||  ||  || [http://partsregistry.org/Part:BBa_I719022 BBa_I719022] || cI with GFP || pSB1A2 || AmpR || High || 933bp || 3988bp ||
+|| A || W || G || S || || [http://partsregistry.org/Part:BBa_I791005 BBa_I791005] || T7 promoter || pSB1A2 || AmpR || High || 23bp || 2102bp ||
 |- style="background:#FFFFBB" align="center"
-||  ||  ||  ||  ||  || BBa_I791021 || luxI coding region under ptet || pSB1A2 || AmpR || High || 860bp || 2939bp ||
+|| 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 ||
-|- style="background:#FFFFBB" align="center"
-||  ||  ||  ||  ||  || BBa_I791??? || DsRed Express under ptet || pSB1A2 || AmpR || High ||  ||  ||
 |- style="background:#FFFFBB" align="center"
 ||  ||  ||  ||  ||  ||  ||  ||  ||  ||  ||  ||  ||
 |}
-<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>
 ===Part Graveyard===
@@ Line 280: / Line 274: @@
 |- style="background:#DDDDDD" align="center"
-|| A ||  || 26 || BBa_S03119 || ptet-LuxR || pSB1A2 || XL1, Midi || 998bp || not used in design
+|| A ||  || 26 || BBa_S03119 || ptet-LuxR || pSB1A2 || 998bp || XL1, Midi || not used in design
 |- style="background:#DDDDDD" align="center"
-|| A ||  || 27 || pSB1A3 || pSB1A3 || pSB1A3 || failed-XL1 || 2157bp || biobrick not present
+|| A ||  || 27 || pSB1A3 || pSB1A3 || pSB1A3 || 2157bp || failed-XL1 || biobrick not present
 |- style="background:#DDDDDD" align="center"
@@ Line 294: / Line 288: @@
 ||  ||  ||  ||  ||  ||  ||  ||  ||
 |}
+<br clear="all">
+<center>| [[Imperial/Wet_Lab| Wet Lab >>]]</center>

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Imperial/Wet Lab/DNA Constructs

From 2007.igem.org

Latest revision as of 02:16, 27 October 2007

Wet Lab: DNA Constructs

Constructs Overview

Cloning Table

Ligation Table

Parts from the Registry

Our Parts

Part Graveyard