Team:Kyoto/Notebook/Construction

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(Difference between revisions)

Revision as of 09:13, 17 October 2010

LastModified: 2010-10-17

1 Notebook: Construction for Lysisbox
2 Tuesday, July 20 By: Wataru, Tomo, Yuki, Kazuya, Ken, Makoto=
- 2.1 Transformation=
3 Wednesday, July 21 By: Wataru, Ken, Makoto, Takuya Y.=
- 3.1 Culture at 37℃ from 07/21 20:50 to 07/22 17:00 and Making Master Plate=
- 3.2 Transformation=
- 3.3 PCR for SRRz and S=
4 Thursday, July 22 By: Wataru=
- 4.1 Electrophoresis (40min) of the PCR Products=
- 4.2 Miniprep=
- 4.3 Culture from 07/22 17:00 to 07/23 10:00 and Making Master Plates of <partinfo>pSB4K5</partinfo> and <partinfo>B0015</partinfo>=
5 Friday, July 23 By: Wataru, Tomo, Makoto=
- 5.1 Miniprep=
- 5.2 PCR Purification=
- 5.3 Standard PCR for SRRz=
- 5.4 Restriction Digestion and Electrophoresis (35min) to check function of our Restriction Enzyme=
- 5.5 Restriction Digestion and Ligation to insert S gene to <partinfo>E0840</partinfo>=
6 Monday, July 26 By: Wataru, Tomonori, Makoto=
- 6.1 Electrophoresis of PCR Products=
- 6.2 PCR Purification=
- 6.3 Transformation=
- 6.4 Culture of <partinfo>pSB4K5</partinfo>, <partinfo>E0840</partinfo>, and <partinfo>B0015</partinfo>=
7 Tuesday, July 27 By: Wataru, Tomo, Kazuya, Ken, Naoi=
- 7.1 Colony PCR of S_Sam7-E0840 (Electrophoresis for 35min)=
- 7.2 Miniprep=
- 7.3 Restriction Digestion=
- 7.4 Ligation=
- 7.5 Transformation=
8 Wednesday, July 28 By: =
- 8.1 Miniprep=
- 8.2 Deletion PCR to delete a functional domain of S gene=
- 8.3 Restriction Digestion to check the function of DpnI=
- 8.4 Electrophoresis for 35min=
9 Thursday, July 29 By: =
- 9.1 Restriction Digestion=
- 9.2 Ligation and Phosphorylation=
- 9.3 Transformation=
10 Monday, August 2 By: Wataru, Ken=
- 10.1 Miniprep=
- 10.2 Standard PCR of <partinfo>E0240</partinfo>=
- 10.3 Electrophoresis=
- 10.4 PCR Purification=
- 10.5 Restriction Digestion for inserting <partinfo>E0240</partinfo> to pSB4K5 by 3A assembly=
- 10.6 PCR Purification=
- 10.7 Error PCR=
- 10.8 Transformation=
11 Tuesday, August 3 By: =
- 11.1 Culture of each two colonies of S_ΔTMD1-E0840₁-1 and S_ΔTMD1-E0840₂ for 37℃ 08/03-08/04=
- 11.2 Miniprep for Construction of Measure(lacP) and Measure(Standard)=
- 11.3 Restriction Digestion=
- 11.4 PCR Purification=
- 11.5 Ethanol Precipitation=
- 11.6 Dilution of <partinfo>pSB4K5</partinfo> by 2µl MilliQ=
- 11.7 Ligation=
- 11.8 Standard PCR of <partinfo>J23101</partinfo>-<partinfo>E0240</partinfo> that is important in the measurement of RPU=
- 11.9 PCR Purification=
- 11.10 Restriction Digestion=
- 11.11 PCR Purification=
- 11.12 Ligation=
- 11.13 Transformation=
12 Thursday, August 5 By: =
- 12.1 Result of Transformation=
13 Friday, August 6=
- 13.1 Miniprep=
- 13.2 Restriction Digestion=
  - 13.2.1 Electrophoresis
- 13.3 Error PCR (Retry)=
- 13.4 Transformation=
14 Monday, August 9 By: Wataru, Tomonori, Ken, Takuya=
- 14.1 Miniprep of MS and ML=
- 14.2 Transfotrmation of MS and ML=
- 14.3 Restriction enzyme digestion and ethanol precipitation=
- 14.4 Ligation and Transformation=
- 14.5 Making culture plate on lac p (low), MS and ML=
- 14.6 Minprep of ΔTMD1+GFP=
- 14.7 Culture and Master Plate=
- 14.8 Miniprep of C2+lac(low), S-R-Rz 1', 3'=
- 14.9 Restriction Digestion and electrophoresis of lac (low) 1 and 3=
- 14.10 Screening PCR of SRRz=
15 Thursday, August 12 By: Wataru, Ken=
- 15.1 Restriction Digestion and electrophoresis of <partinfo>B0015</partinfo>=
- 15.2 Miniprep of SΔTMD1GFP=
- 15.3 Point mutation PCR of ΔTMD1GFP=
- 15.4 Restriction Digestion(DpnI): 17:50-18:50=
- 15.5 Electrophoresis=
- 15.6 Ligation and Transformation=
16 Monday, August 23 By: Wataru, Tomo, Ken, Fumitaka, Tasuku=
- 16.1 Miniprep of ΔTMD1=
- 16.2 Sequencing of ΔTMD1 and MS=
- 16.3 Screening PCR of SRRz-DT=
- 16.4 Deletion PCR of rΔTMD1GFP 2-2=
- 16.5 Restriction Digestion(DpnI)=
- 16.6 Ligation=
- 16.7 Transformation=
17 Tuesday, August 24 By:Ken, Tomo, Tasuku, Takuya=
- 17.1 Retry of deletion PCR of rδTMD1 GFP=
- 17.2 Restriction Digestion (DpnI)=
- 17.3 Electrophoreis=
- 17.4 Ligation=
- 17.5 Point mutation of SRRz=
- 17.6 Restriction Digestion(DpnI), electrophoresis and ligation=
18 PCR of E0240=
19 PCR Purification=
- 19.1 Restriction Digestion(EcoRI, PstI) and Gel extraction=
- 19.2 Transformation=
20 Wednesday, August 25 By:Ken, Tomo, Kazuya, Tasuku, Takuya=
- 20.1 Making culture and Master plate=
- 20.2 Miniprep of 1-5G=
- 20.3 Restriction Digestion and purification of 1-5G(low copy plasmid) and lac low=
- 20.4 Ligation of <partinfo>E0240</partinfo> and <partinfo>pSB4K5</partinfo>, Transformation=
- 20.5 Miniprep=
- 20.6 Restriction Digestion of constP(0.7)=
- 20.7 Purification of constP (0.7)=
21 Friday, August 27 By:Ken, Tomo, Kazuya, Fumitaka=
- 21.1 Making master plate of E0240 low=
- 21.2 Restriction Digestion of rrΔTMD1 and rSRRz=
- 21.3 Purification=
- 21.4 Lagation and transformation=
22 Monday, August 30 By: Tomonori, Kazuya, Tasuku, Ken=
- 22.1 Making culture and Master plate=
- 22.2 Miniprep=
- 22.3 RE of constP (0.3) and lac rrΔTMD1=
- 22.4 Gel Extraction of lac rrΔTMD1=
- 22.5 Purification of constP (0.3) and lac rrΔTMD1=
- 22.6 Ligation and transformation=
- 22.7 Making culture and Master plate=
- 22.8 Miniprep=
- 22.9 Restriction Digestion of rSRRz and low=
- 22.10 Purification=
- 22.11 Ligation and transformation=
23 Thursday, September 2 By: Tomonori, Tomo, Takuya, Ken=
- 23.1 Making culture and Master plate=
- 23.2 Screening PCR of rSRRz low=
24 Friday, September 3 By: Tomonori, Tomo, Kazuya, Tasuku, Fumitaka, Ken=
- 24.1 Making culture=

Notebook: Construction for Lysisbox

Tuesday, July 20 By: Wataru, Tomo, Yuki, Kazuya, Ken, Makoto=

Transformation=

Name	Well	Sample	Competent Cells	Total	Plate	Incubation	Result
<partinfo>J23100</partinfo>	1-18-C	1 µl	20	21	LB (Amp+)	At 37℃, 7/20 20:50 - 7/21 17:00	○
<partinfo>J23105</partinfo>	1-18-M	1	20	21			○
<partinfo>J23116</partinfo>	1-20-M	1	20	21			○
<partinfo>R0011</partinfo>	1-6-G	1	20	21			○
<partinfo>E0840</partinfo>	1-12-O	1	20	21			○
<partinfo>J06702</partinfo>	2-8-E	1	20	21			○
<partinfo>pSB4K5</partinfo>	1-5-G	1	20	21			×
<partinfo>B0015</partinfo>	1-23-L	1	20	21	LB (Kan+)		×

A vector of <partinfo>pSB4K5</partinfo> is Kanamycin-resistance, however, we plated it to LB plate (Amp+). And We didn't pre-culture <partinfo>B0015</partinfo> despite its vector is Kanamycin-resistance. So, it was predicted that we will fail the transformation of <partinfo>pSB4K5</partinfo> and <partinfo>B0015</partinfo>.

Wednesday, July 21 By: Wataru, Ken, Makoto, Takuya Y.=

Culture at 37℃ from 07/21 20:50 to 07/22 17:00 and Making Master Plate=

Transformation=

Name	Well	Sample	Competent Cells	Total	Plate	Incubation	Result
<partinfo>pSB4K5</partinfo>	1-5-G	1 µl	20	21	LB (Kan+)	At 37℃, 7/21 20:50 - 7/22 16:30	○
<partinfo>B0015</partinfo>	1-23-L	1	20	21	LB (Kan+)	At 37℃, 7/21 20:50 - 7/22 16:30	○

PCR for SRRz and S=

No.	Water	MgSO4	dNTPs	10xBuffer	Template DNA	Primer Fwd.	Primer Rev. (SRRz)	Primer Rev. (S)	KOD Plus ver.2	Total
1	28 µl	3	5	5	5	1.5	1.5	-	1	50
2	28	3	5	5	5	1.5	1.5	-	1	50
3	28	3	5	5	5	1.5	-	1.5	1	50
4	28	3	5	5	5	1.5	-	1.5	1	50
5	28	3	5	5	5	1.5	1.5	-	1	50
6	28	3	5	5	5	1.5	1.5	-	1	50
7	28	3	5	5	5	1.5	-	1.5	1	50
8	28	3	5	5	5	1.5	-	1.5	1	50

94℃	2min
98℃	10sec	30 cycles
55℃	30sec
68℃	4min
4℃	forever

Thursday, July 22 By: Wataru=

Electrophoresis (40min) of the PCR Products=

No.	Name	Length(bp)	Result
1	SRRz	1386	○
2	SRRz	1386	○
3	S	442	○
4	S	442	○
5	SRRz	1386	○
6	SRRz	1386	○
7	S	442	○
8	S	442	○

Marker: 100bp, 1kb, 1kb, 100bp.

Miniprep=

Name	Concentration
<partinfo>J23100</partinfo>	18.5 (ng/µl)
<partinfo>J23105</partinfo>	12.5
<partinfo>J23116</partinfo>	14.6
<partinfo>R0011</partinfo>	8.6
<partinfo>E0840</partinfo>	12.1
<partinfo>J06702</partinfo>	14.7

The concentration of all samples was very week. Probably our shaking incubation was week.

Culture from 07/22 17:00 to 07/23 10:00 and Making Master Plates of <partinfo>pSB4K5</partinfo> and <partinfo>B0015</partinfo>=

Friday, July 23 By: Wataru, Tomo, Makoto=

Miniprep=

Name	Concentration
<partinfo>pSB4K5</partinfo>	79.2 (ng/µl)
<partinfo>B0015</partinfo>	-

We lost <partinfo>B0015</partinfo> by our mistake. The concentration of <partinfo>pSB4K5</partinfo> is high, so this condition of shaking incubation is moderate.

PCR Purification=

No.	Name	Concentration	New Name
1	SRRz	18.6 ng/µl	-
3	S	77.6	S_Sam7(1)
5	SRRz	33.6	-
7	S	65.4	S_Sam7(2)

The concentration of sample number 1 and 5, the PCR products of S-R-Rz/Rz1, is week, so we desided to retry PCR.

Standard PCR for SRRz=

No.	Water	MgSO4	dNTPs	10xBuffer	Template DNA	Primer Fwd. (SRRz)	Primer Rev. (SRRz)	KOD plus ver.2	Total
1	28 µl	3	5	5	5	1.5	1.5	1	50
2	28	3	5	5	5	1.5	1.5	1	50
3	26.5	4.5	5	5	5	1.5	1.5	1	50
4	26.5	4.5	5	5	5	1.5	1.5	1	50
5	25	6	5	5	5	1.5	1.5	1	50
6	25	6	5	5	5	1.5	1.5	1	50

94℃	2min
98℃	10sec	30 cycles
55℃	30sec
68℃	4min
4℃	forever

Restriction Digestion and Electrophoresis (35min) to check function of our Restriction Enzyme=

No.	Name	Sample	10xBuffer	BSA	Enzyme		MilliQ	Total	Incubation
1	<partinfo>J06702</partinfo>	5 µl	1	0.1	EcoRI	0.1	3.6	10	At 37℃ 7/23 18:00 - 7/23 18:30
2	<partinfo>J06702</partinfo>	5	1	0.1	XbaI	0.1	3.6	10
3	<partinfo>J06702</partinfo>	5	1	0.1	SpeI	0.1	3.6	10
4	<partinfo>J06702</partinfo>	5	1	0.1	PstI	0.1	3.6	10
5	<partinfo>J06702</partinfo>	5	1	0.1	-		3.7	10

Marker: 1kb. Comparison to No. 5 (control, circular DNA), the bands of No. 1, 2, 3, and 4 was shifted. The DNA of them was linearized by Restriction enzymes. So, our restriction enzymes work correctly.

Restriction Digestion and Ligation to insert S gene to <partinfo>E0840</partinfo>=

Name	Sample	10xBuffer	Enzyme 1		Enzyme 2		MilliQ	Total	Incubation
S_Sam7(1)	11 µl	5	EcoRI	0.2	SpeI	0.2	33.6	50	At 37℃ for 2h
S_Sam7(2)	11	5	EcoRI	0.2	SpeI	0.2	33.6	50
<partinfo>E0840</partinfo>	45	5	EcoRI	0.2	XbaI	0.2	0	50

After PCR Purification, evaporated them and diluted 3ul.

Name	Vector		Insert		Ligation High	Total
S_Sam7(1)-E0840	<partinfo>E0840</partinfo>	0.5µl	S_Sam7(1)	0.5	1	2
S_Sam7(2)-E0840	<partinfo>E0840</partinfo>	0.5	S_Sam7(2)	0.5	1	2

Monday, July 26 By: Wataru, Tomonori, Makoto=

Electrophoresis of PCR Products=

No.	Name	Length(bp)
1	SRRz	1386
2	SRRz	1386
3	SRRz	1386
4	SRRz	1386
5	SRRz	1386
6	SRRz	1386

Marker: 1kb. At the condition 4 (4.5µl MgSO4) and 6 (6µl MgSO4), SRRz is amplified very much. So we decided to use them.

PCR Purification=

No.	Name	Concentration	New Name
4	SRRZ	51.6 ng/µl	SRRz_Sam7(1)
5	SRRZ	59.3
6	SRRZ	59.6	SRRz_Sam7(2)

Transformation=

Name	Well	Sample	Competent Cell	Total	Plate	Incubation	Result
<partinfo>E0240</partinfo>	1-12-M	1 µl	20	21	LB (Amp+)	At 37℃ 7/26 - 7/27	×
<partinfo>I20260</partinfo>	2-17-F	1	20	21	LB (Kan+)		×
<partinfo>J04450</partinfo>	1-5-E	1	20	21	LB (Kan+)		×

Culture of <partinfo>pSB4K5</partinfo>, <partinfo>E0840</partinfo>, and <partinfo>B0015</partinfo>=

Tuesday, July 27 By: Wataru, Tomo, Kazuya, Ken, Naoi=

Colony PCR of S_Sam7-E0840 (Electrophoresis for 35min)=

No.	Name	Length	Result
1	S_Sam7(1)-E0840	1522	○
2	S_Sam7(1)-E0840	1522	×
3	S_Sam7(1)-E0840	1522	○
4	S_Sam7(1)-E0840	1522	×
5	S_Sam7(1)-E0840	1522	○
6	S_Sam7(1)-E0840	1522	◎ (Use as S_Sam7(1)-E0840)
7	S_Sam7(2)-E0840	1522	×
8	S_Sam7(2)-E0840	1522	×
9	S_Sam7(2)-E0840	1522	×
10	S_Sam7(2)-E0840	1522	×
11	S_Sam7(2)-E0840	1522	◎ (Use as S_Sam7(2)-E0840)
12	S_Sam7(2)-E0840	1522	○
13	S_Sam7(2)-E0840	1522	○
+	<partinfo>E0840</partinfo>	1116
-	None

Marker: 1kb, 100bp

Miniprep=

Name	Concentration
<partinfo>R0011</partinfo>	26.9 ng/µl
<partinfo>B0015</partinfo>	120.0
<partinfo>E0840</partinfo>	120.1

Restriction Digestion=

	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total	Incubation
<partinfo>B0015</partinfo>	30 µl	5	0.5	EcoRI	0.4	XbaI	0.3	13.7	50	At 37℃ 16:45 - 18:00
SRRz_Sam7(1)	40	5	0.5	EcoRI	0.4	SpeI	0.4	3.8	50
SRRz_Sam7(2)	40	5	0.5	EcoRI	0.4	SpeI	0.4	3.8	50

Ligation=

Transformation=

Name	Sample	Competent Cells	Total	Plate	Incubation	Result
SRRz_Sam7(1)-B0015						○
SRRz_Sam7(2)-B0015						○

Wednesday, July 28 By: =

Miniprep=

Name	Concentration
S_Sam7(1)-E0840	95.5 ng/µl
S_Sam7(2)-E0840	98.6

Diluted S_Sam7(1)-E0840 and S_Sam7(2)-E0840 20 times with water, and used as template DNA.

Deletion PCR to delete a functional domain of S gene=

	Water	MgSO4	dNTPs	10xBuffer	Primer Fwd.	Primer Rev.	S_Sam7(1)-E0840	S_Sam7(2)-E0840	KOD Plus ver.2	Total
S_Sam7,ΔTMD1(1)-E0840 (1)	28	3	5	5	1.5	1.5	5	-	1	50
S_Sam7,ΔTMD1(1)-E0840 (2)	28	3	5	5	1.5	1.5	5	-	1	50
S_Sam7,ΔTMD1(2)-E0840 (1)	28	3	5	5	1.5	1.5	-	5	1	50
S_Sam7,ΔTMD1(2)-E0840 (2)	28	3	5	5	1.5	1.5	-	5	1	50

94℃	2min
98℃	10sec	35 cycles
55℃	30sec
68℃	4min
4℃	forever

Restriction Digestion to check the function of DpnI=

Name	Sample	fast digestion buffer	DpnI	MilliQ	Total
S_Sam7,ΔTMD1(1)-E0840 (1)	3	1	0.1	5.8	10
S_Sam7,ΔTMD1(2)-E0840 (2)	3	1	0.1	5.8	10

Electrophoresis for 35min=

No.	Name	Length
1	Not digested S_Sam7(1)-E0840	3363
2	Not digested S_Sam7(2)-E0840	3363
3	Digested S_Sam7(1)-E0840	1021, 933, 402, 341, 258, 105, ...
4	Digested S_Sam7(2)-E0840	1021, 933, 402, 341, 258, 105, ...

Marker: 1kb, 100bp DpnI works correctly.

Thursday, July 29 By: =

Restriction Digestion=

Name	Sample volume	Fastdigestion Buffer	Enzyme 1		MilliQ	Total	Incubation
S_Sam7,ΔTMD1(1)-E0840 (1)	50 µl	6	DpnI	0.2	3.8	60	07/29 09:40 - 07/29 11:00
S_Sam7,ΔTMD1(2)-E0840 (1)	50	6	DpnI	0.2	3.8	60	07/29 09:40 - 07/29 11:00

Ligation and Phosphorylation=

Name	Sample	MilliQ	Ligation High	T4 Kinase	Total	Incubation
S_Sam7,ΔTMD1(1)-E0840 (1)	2 µl	7	5	1	15	07/29 11:30 ~ 07/29 13:00
S_Sam7,ΔTMD1(1)-E0840 (2)	2	7	5	1	15	07/29 11:30 ~ 07/29 13:00

Transformation=

Name	Sample Volume	Competent Cell	Total	Plate	Incubation	Result
S_Sam7,ΔTMD1(1)-E0840 (1)	3 µl	30	33	LB Amp+	07/29 ~ 07/30	○
S_Sam7,ΔTMD1(1)-E0840 (2)	3	30	33	LB Amp+	07/29 ~ 07/30	○

Monday, August 2 By: Wataru, Ken=

Miniprep=

Name	Concentration(ng/µL)
S_ΔTMD1-E0840-1	52.7
S_ΔTMD1-E0840-2	54.4
S_ΔTMD1-E0840-3	89.5
<partinfo>pSB4K5</partinfo>	50.7
<partinfo>R0011</partinfo>	18.6

Standard PCR of <partinfo>E0240</partinfo>=

E240 is very important parts to measure RPU of promoters in iGEM. However, we failed to transfect it to E.coli from parts kit of iGEM. So we decided to amplify this parts by PCR.

Name	Water	25mM MgSO4	2mM dNTPs	10xBuffer for KOD Plus ver.2	Primer VF2(10µM)	Primer VR(10µM)	Template E240	KOD Pllus ver.2	Total
E0240₁	28	3	5	5	1.5	1.5	5	1	50
E0240₂	28	3	5	5	1.5	1.5	5	1	50

94℃	2min
98℃	10sec	35 cycles
55℃	30sec
68℃	4min
4℃	forever

Electrophoresis=

PCR Purification=

Sample number	Concentration(ng/µL)
E0240₁	42.6
E0240₂	55.3

Restriction Digestion for inserting <partinfo>E0240</partinfo> to pSB4K5 by 3A assembly=

Name	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
E0240₁(X-P)	30	5	0.5	XbaI	0.2	PstI	0.2	14.1	50
E0240₂(X-P)	30	5	0.5	XbaI	0.2	PstI	0.2	14.1	50

PCR Purification=

Name	Concentration(ng/µL)	Volume(µL)
E0240₁(X-P)	21.8	40
E0240₂(X-P)	32.4	45

Stored at -20℃.

Error PCR=

Name	Water	25mM MgSO4	2mM dNTPs	10xBuffer for KOD Plus ver.2	Primer VF2(10µM)	Primer VR(10µM)	Template Δ1	Template	Template	KOD Pllus ver.2	Total
S_ΔTMD1-E0840₁-1	32	3	5	5	1.5	1.5	1	-	-	1	50
S_ΔTMD1-E0840₁-2	32	3	5	5	1.5	1.5	-	1	-	1	50
S_ΔTMD1-E0840₂	32	3	5	5	1.5	1.5	-	-	1	1	50

94℃	2min
98℃	10sec	20 cycles
68℃	4min	20 cycles
4℃	forever

Transformation=

Name	Sample (µl)	Competent Cells (µl)	Total (µl)	Plate	Incubation	Result
S_ΔTMD1-E0840₁-1	2	20	22	rowspan="3"	rowspan="3"	○
S_ΔTMD1-E0840₁-2	2	20	22	}
S_ΔTMD1-E0840₂	2	20	22	○

Tuesday, August 3 By: =

Culture of each two colonies of S_ΔTMD1-E0840₁-1 and S_ΔTMD1-E0840₂ for 37℃ 08/03-08/04=

Miniprep for Construction of Measure(lacP) and Measure(Standard)=

Sample number	Concentration(ng/µL)
<partinfo>pSB4K5</partinfo>	60.7
<partinfo>R0011</partinfo>	26.8

Restriction Digestion=

Name	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
R0011	50	6	0.6	EcoRI	0.2	SpeI	0.2	3	60
pSB4K5(E-P)	50	6	0.6	EcoRI	0.2	PstI	0.2	3	60
E0240₁(X-P)	50	6	0.6	XbaI	0.2	PstI	0.2	3	60
E0240₂(X-P)	50	6	0.6	XbaI	0.2	PstI	0.2	3	60

PCR Purification=

Sample number	Concentration(ng/µL)
pSB4K5(E-P)	39.5
E0240₁(X-P)	21.8
E0240₂(X-P)	32.4

pSB4K5(E-P) is concentrated 10µL and E0240₁(X-P), E0240₂(X-P) are concentrated 1µL.

Ethanol Precipitation=

Dilution of <partinfo>pSB4K5</partinfo> by 2µl MilliQ=

Ligation=

	Vector	Insert 1		Insert 2		Ligation High	Total	Incubation
R0011-E0240₁[Low]	pSB4K5(E-P)	1	R0011(E-S)	1	E0240₁(X-P)	1	3	15	17:30 - 20:20
R0011-E0240₂[Low]	pSB4K5(E-P)	1	R0011(E-S)	1	E0240₂(X-P)	1	3	15	17:30 - 20:20

Standard PCR of <partinfo>J23101</partinfo>-<partinfo>E0240</partinfo> that is important in the measurement of RPU=

Name	Water	25mM MgSO4	2mM dNTPs	10xBuffer for KOD Plus ver.2	Primer VF2(10µM)	Primer VR(10µM)	Template J23101-E0240	KOD plus ver.2	Total
J23101-E0240₁	32	3	5	5	1.5	1.5	1	1	50
J23101-E0240₂	32	3	5	5	1.5	1.5	-	1	50

94℃	2min
98℃	10sec	30 cycles
55℃	30sec
68℃	4min
4℃	forever

PCR Purification=

Name	Concentration(ng/µL)
J23101-E0240	40.6

Restriction Digestion=

Name	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
J23101-E0240(E-P)	45	6	0.6	EcoRI	0.2	PstI	0.2	8	60

PCR Purification=

Name	Concentration(ng/µL)	Volume(µL)
J23101-E0240(E-P)	74.1	30

J23101-E0240(E-P) is concentrated 7µL

Ligation=

	Vector	Insert		Ligation High		Total	Incubation
J23101-E0240[Low]	pSB4K5(E-P)	1	J23101-E0240(E-P)	1	2	4	20:00-20:30

Transformation=

Name	Conc(/µL)	Sample Volume(µL)	Competent Cell(µL)	Total	Plate	Incubation
R0011-E0240₁[Low]	-	1	20	21	LB kan	8/3~8/4
R0011-E0240₂[Low]	-	1	20	21
J23101-E0240[Low]	-	1	20	21

Thursday, August 5 By: =

Result of Transformation=

R0011-E0240₁[Low]	Many colonies
R0011-E0240₂[Low]
J23101-E0240[Low]

pSB4K5 is inserted RFP generator. We didn't distinguish this inserted parts from low copy plasmid backbone, so self-ligated colony is red. So, white colony is correctly inserted parts. However, white colonies and green colonies are observed in R0011-E0240₁[Low] and R0011-E0240₂[Low] plate. We cultured both white and green colonies. In J23101-E0240[Low], Many of colonies are red, but green colonies are observed. We cultured green colonies.

Name	Color	Incubation
R0011-E0240₁[Low]-1	Green Colony	8/5-8/6
R0011-E0240₁[Low]-2	Green Colony
R0011-E0240₁[Low]-3	White Colony
R0011-E0240₁[Low]-4	White Colony
R0011-E0240₂[Low]-1	Green Colony
R0011-E0240₂[Low]-2	White Colony
R0011-E0240₂[Low]-3	White Colony
R0011-E0240₂[Low]-4	White Colony
J23101-E0240[Low]-1	Green Colony
J23101-E0240[Low]-2	Green Colony
J23101-E0240[Low]-3	Green Colony

Name	Concentration(ng/µL)
S_ΔTMD1-E0840₁-1-A	28.9
S_ΔTMD1-E0840₁-1-B	25.3
S_ΔTMD1-E0840₂-A	26.6
S_ΔTMD1-E0840₂-B	24.0

As a result, deletion is succeeded, however, point mutation is failed. It is because DpnI is too little to digest all of template DNA.

Friday, August 6=

Miniprep=

Name
R0011-E0240₁[Low]-1
R0011-E0240₁[Low]-2
R0011-E0240₁[Low]-3
R0011-E0240₁[Low]-4
R0011-E0240₂[Low]-1
R0011-E0240₂[Low]-2
R0011-E0240₂[Low]-3
R0011-E0240₂[Low]-4
J23101-E0240[Low]-1
J23101-E0240[Low]-2
J23101-E0240[Low]-3

Restriction Digestion=

Name	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
R0011-E0240₁[Low]-1	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₁[Low]-2	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₁[Low]-3	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₁[Low]-4	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₂[Low]-1	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₂[Low]-2	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₂[Low]-3	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240₂[Low]-4	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
J23101-E0240[Low]-1	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
J23101-E0240[Low]-2	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
J23101-E0240[Low]-3	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60

Electrophoresis

M	100bp	colspan="4"	colspan="4"\|
M	λ
M	λ
M	100bp
1	J23101-E0240[Low]-1
2	J23101-E0240[Low]-2
3	J23101-E0240[Low]-1
4	R0011-E0240₁[Low]-1		○
5	R0011-E0240₁[Low]-2		○
6	R0011-E0240₁[Low]-3		}
7	R0011-E0240₁[Low]-4		}
8	R0011-E0240₂[Low]-1		○
9	R0011-E0240₂[Low]-2		}
10	R0011-E0240₂[Low]-3		}
11	R0011-E0240₂[Low]-4		}
12	J23101-E0240[Low]-1		○
13	J23101-E0240[Low]-2		○

White colonies are not inserted <partinfo>R0011</partinfo> but its vector. Top10 we used are deleted Lac operon. Then, correctly inserted parts is green because of the lack of lacI gene.

Error PCR (Retry)=

Name	Water	25mM MgSO4	2mM dNTPs	10xBuffer for KOD Plus ver.2	Primer VF2(10µM)	Primer VR(10µM)	Template ΔTMD failed(50ng/µL)	KOD plus ver.2	Total
ΔTMD①	32	3	5	5	1.5	1.5	1	1	50
ΔTMD②	32	3	5	5	1.5	1.5	1	1	50

94℃	2min
98℃	10sec	25 cycles
68℃	4min	25 cycles
Add DpnI 2µl
Incubate	1h
4℃	forever

Transformation=

Name	Conc(/µL)	Sample Volum(µL)	Competent Cell(µL)	Total	Plate	Incubation
ΔTMD①	-	4	50	54	LB kan	8/6~8/9
ΔTMD②	-	4	50	54
2-17-F	-	2	50	52
2-I-5		2	50	52	LB amp

Monday, August 9 By: Wataru, Tomonori, Ken, Takuya=

Miniprep of MS and ML=

Sample number	concentration(ng/µL)
MS	116.2
ML	146.6

Transfotrmation of MS and ML=

Sample	conc(ng/µL)	Sample vol(µL)	Competent Cell	Competent cell vol(µL)	Total vol(µL)	Plate	Incuvation
MS	116.2	2	KRX	50	52	LB kanamycin	8/9 18:00‾8/10 12:00
ML	146.6	2	KRX	50	52	LB kanamycin	8/9 18:00‾8/10 12:00

Restriction enzyme digestion and ethanol precipitation=

To use lac p for next ligation, we digested 1-6-G by EroRI and PstI

Sample	10x Buffer	BSA	Enzyme (EcoRI)	Enzyme (PstI)	MilliQ	Total
50	6	0.6	0.5	0.5	2.4	60

Incubate 37℃ 8/9 16:20‾18:20 After restriction enzyme digestion, we did ethanol precipitation.

Ligation and Transformation=

Sample	Conc (nu/µL)	Sample vol (µL)	Competent cell	Competent cell vol (µL)	Total vol (µL)	Plate	Incuvation
Lac p (low)	-	2	KRX	50	52	LB kanamycin	8/9 20:00‾8/10 9:00
Lac p (low)	-	2	C2	50	52	LB kanamycin	8/9 20:00‾8/10 9:00

==Tuesday, August 10 By: Wataru, Tomonori, Ken, Fumitaka

Making culture plate on lac p (low), MS and ML=

Lac p (low)	KRX	Many colonies
Lac p (low)	C2
MS	KRX
ML	KRX

Minprep of ΔTMD1+GFP=

Sample number	Concentration (ng/µL)
1-1	9.9
1-2	27.3
2-1	43.2
2-2	34.7

37℃ 8/9 18:00‾8/10 9:00

Culture and Master Plate=

==Wednesday, August 11 By: Wataru, Naoi, Ken, Takuya

Sample	Medium	Cloud	Incubation
1	Kanamycin	o	37℃8/10 20:00‾8/11 9:00
1	Ampicillin	x
2	Kanamycin	o
2	Ampicillin	o
3	Kanamycin	o
3	Ampicillin	x
4	Kanamycin	o
4	Ampicillin	x
5	Kanamycin	o
5	Ampicillin	x
6	Kanamycin	o
6	Ampicillin	o
7	Kanamycin	o
7	Ampicillin	x

Discussion: About sample 1, 3, 4, 5 and 7, lac promoter was correctly inserted in low copy plasmid. About sample 2 and 6, low copy plasmid and vector derived from lac promoter were ligated. We decided to use sample 1 or 3.

Miniprep of C2+lac(low), S-R-Rz 1', 3'=

lac(low)1 : 31.2 (ng/µL) lac(low)2 : 29.9 (ng/µL)

Restriction Digestion and electrophoresis of lac (low) 1 and 3=

Name	EcoRI	PstI
1	0.2	-
2	-	0.2
3	0.2	0.2
N	-	-

Sample: 1-1, 1-2, 1-3, 1-N, 3-1, 3-2, 3-3, 3-N M 1-1 1-2 1-3 1-N M M 3-1 3-2 3-3 3-N M Discussion: Each enzyme correctly cut samples.

Screening PCR of SRRz=

Sample: 1-20 Control: P(1-23L) P'(2-8E) N Maker: lambda M N P P' P 1 2 3 4 5 6 M 7 8 9 10 11 12 13 M 14 15 16 18 19 20 M Discussion: All of the sample were self-ligation of DT and SRRz weren't inserted.

Thursday, August 12 By: Wataru, Ken=

Restriction Digestion and electrophoresis of <partinfo>B0015</partinfo>=

Sample name	Template	10xbuffer	100xbuffer	EcoRI	XbaI 1	XbaI 2	SpeI	PstI 1	PstI 2	Water	Total
1	3	1	0.1	0.2	-	-	-	-	-	5.7	10
2	3	1	0.1	-	0.2	-	-	-	-	5.7	10
3	3	1	0.1	-	-	0.2	-	-	-	5.7	10
4	3	1	0.1	-	-	-	0.2	-	-	5.7	10
5	3	1	0.1	-	-	-	-	0.2	-	5.7	10
6	3	1	0.1	-	-	-	-	-	0.2	5.7	10
N	3	1	0.1	-	-	-	-	-	-	5.9	10

Sample: 1-6, N Maker: lambda, 100 M 1 2 3 4 5 6 N M M M Discussion: Each enzyme correctly cut each sample and was active.

==Thursday, August 19 By: Wataru, Tomo, Ken

Miniprep of SΔTMD1GFP=

29.6(ng/µg)

Point mutation PCR of ΔTMD1GFP=

Sample number	Template	10xbuffer	dNTPs	MgSO4	Primer 1	Primer 2	Water	KOD-plus-	Total
1	1.5	5	5	3	1.5	1.5	31.5	1	50
2	1.5	5	5	3	1.5	1.5	31.5	1	50
control	1.5	5	5	3	1.5	1.5	32.5	-	50

94(℃)	2min
98	10sec	30cycles
55	30sec
68	3.5min
4.0	forever

Restriction Digestion(DpnI): 17:50-18:50=

Electrophoresis=

Sample: 1, 2, Control Marker: lambda, 100

Ligation and Transformation=

We named point mutation PCR products rΔTMD1GFP.

Monday, August 23 By: Wataru, Tomo, Ken, Fumitaka, Tasuku=

Miniprep of ΔTMD1=

Sample number	Concentration(ng/µg)
1-1	58.9
2-2	49.9

Sequencing of ΔTMD1 and MS=

Sample: rδTMD1GFP1-1, 2-2, and MS Discussion: The sequencing was in success and the results were desirable. It meant point mutation of δTMD1GFP was succeeded and sequence of MS was confirmed. We decided to use rδTMD1GFP.

Screening PCR of SRRz-DT=

Sample: 1-13, Marker: lambda and 100, Control:P(1-23L) and N

90℃	10min
94℃	30sec	35cycles
50℃	30sec
72℃	1.5min
72℃	4min
4℃	hold

M 1 2 3 4 5 6 7 8 9 10 11 12 13 P N M Discussion: We found the band; about 200bp, and it meant the lligation was completed successfully.

Deletion PCR of rΔTMD1GFP 2-2=

Sample	10x	dNTPs	Primer1	Primer2	Template	Water	KOD-plus-	Total
1	5	5	1.5	1.5	1	35	1	50
2	5	5	1.5	1.5	1	35	1	50
Control	5	5	1.5	1.5	1	35	-	50

94℃	2min
94℃	10sec	35cycles
56℃	30sec
68℃	3.5min
4℃	hold

Restriction Digestion(DpnI)=

Template	25(µL)
DpnI	1
Total	26

19:10-20:10

Ligation=

Sample	Template	Water	Ligation high	T4 Kinase	total
1	3	6	5	1	15
2	3	6	5	1	15
Control	3	6	5	1	15

20:15-21:15

Transformation=

We named sample 1, 2 and control rrδTMD1GFP1, 2 and control.

Tuesday, August 24 By:Ken, Tomo, Tasuku, Takuya=

Retry of deletion PCR of rδTMD1 GFP=

Sample	10x	dNTPs	MgSO4	Primer1	Primer2	Template	Water	KOD-plus-	Total
1	5	5	3	1.5	1.5	1	32	1	50
2	5	5	3	1.5	1.5	1	32	1	50
Control	5	5	3	1.5	1.5	1	32	1	50

94℃	2min
94℃	10sec	35cycles
58℃	30sec
68℃	3.5min
4℃	hold

Restriction Digestion (DpnI)=

14:15-15:15

Electrophoreis=

Sample: 1, 2, and control, Maker: 100 and lambda M 1 2 C M We found the band of sample 1 and 2 about 3000bp and there wasn't the band of sample control. So, we confirmed the PCR and RE were completed successfully.

Ligation=

Point mutation of SRRz=

Sample	10x	dNTPs	MgSO4	Primer1	Primer2	Template	Water	KOD-plus-	total
1	5	5	3	1.5	1.5	1	32	1	50
2	5	5	3	1.5	1.5	1	32	1	50
control	5	5	3	1.5	1.5	1	32	1	50

94℃	2min
98℃	10sec	30cycles
55℃	30sec
68℃	4min
4℃	hold

Restriction Digestion(DpnI), electrophoresis and ligation=

We could find point mutation PCR and restriction enzyme of DpnI was done.

PCR of E0240=

Sample	10}	dNTPs	MgSO4	VF2	VR	Template	Water	KOD-plus-	Total
1	5	5	3	1.5	1.5	1	31.5	1	50
2	5	5	3	1.5	1.5	1	31.5	1	50

PCR Purification=

Sample1: 5.5*50(ng/µL) Sample2: 5.2*50(ng/µL)

Restriction Digestion(EcoRI, PstI) and Gel extraction=

Sample1: 28.8 (ng/µL) Sample2: 26.4 (ng/µL)

Transformation=

Sample: rrΔTMD1GFP1. 2. control, and rSRRz1. 2. control

Wednesday, August 25 By:Ken, Tomo, Kazuya, Tasuku, Takuya=

Making culture and Master plate=

rrΔTMD1-1	Many Colonies
rrΔTMD1-2	Many Colonies
rrΔTMD1-C-	zero
rSRRz-1	Many Colonies
rSRRz-2	Many Colonies
rSRRz-C-	zero

Miniprep of 1-5G=

29.0 (ng/µL)

Restriction Digestion and purification of 1-5G(low copy plasmid) and lac low=

Sample name	Template	10xbuffer	100xbuffer	EcoRI	SpeI	PstI	Water	Total
1-5G	50	6	0.6	0.4	0.4	-	2.6	60
Lac low	10	4	0.4	-	0.3	0.3	25	40

Sample Name	Concentration(ng/µL)
1-5G	18.4
Lac low	8.6

Ligation of <partinfo>E0240</partinfo> and <partinfo>pSB4K5</partinfo>, Transformation=

==Thursday, August 26 By:Ken, Tomo, Kazuya, Tasuku, Takuya, Fumitaka

Miniprep=

Sample name	Concentration(ng/µL)
constP(0.7)	44.5

Restriction Digestion of constP(0.7)=

Template	10xbuffer	100xbuffer	SpeI	PstI	Water	Total
25	4	0.4	0.3	0.3	10	40

Purification of constP (0.7)=

49.8 ng/µL

Friday, August 27 By:Ken, Tomo, Kazuya, Fumitaka=

Making master plate of E0240 low=

Sample Name	Concentration(ng/µL)
rrΔTMD1 1-2	20.9
rSRRz 1-1	16.4

Restriction Digestion of rrΔTMD1 and rSRRz=

Sample name	Template	10xbuffer	100xbuffer	XbaI	PstI	Water	Total
rrΔTMD1 1-2	45	6	0.6	0.3	0.3	7.8	60
rSRRz 1-1	45	6	0.6	0.3	0.3	7.8	60

(13:20-14:20)

Purification=

rrΔTMD1 1-2	44.7
rSRRz 1-1	56.1

Lagation and transformation=

lacP + rrΔTMD1 1-2 constP (0.7) + rrΔTMD1 1-2 lac low + rSRRz 1-1

Monday, August 30 By: Tomonori, Kazuya, Tasuku, Ken=

Making culture and Master plate=

lacP rrΔTMD1GFP	Many colonies
lacP rrΔTMD1GFP(control)	Some colonies
constP rrΔTMD1GFP	Many colonies
constP rrΔTMD1GFP(control)	Many colonies
lacP rSRRz low	No colony
lacP rSRRz low(control)	No colony

Discussion: There ware some colonies, which emitted green light, on the plate 1. So, we cultured those colonies on master plate. On the plate 5 and 6, even though we used KRX, which is able to repress lac promoter, colonies might be dead. However, we still have to do some experience so that we confirm lac promoter cannot repress enough and E. coli cannot survive.

==Tuesday, August 31 By: Tomonori, Takuya Y., Kazuya, Tasuku, Takuya, Ken

Miniprep=

constP (0.3)	48.5 (ng/µL)
lac rrΔTMD1	107.3

RE of constP (0.3) and lac rrΔTMD1=

Gel Extraction of lac rrΔTMD1=

File:KyotoExp100831-1.png

45min Discussion: There were two band at the bottom of the gel. It was too long -45min-, and insert and vector might be contaminated. But we went on next operation.

Purification of constP (0.3) and lac rrΔTMD1=

constP (0.3)	5.8 (ng/µL)
lac rrΔTMD1	7.8 (ng/µL)

Ligation and transformation=

Insert	Vector
lac rrΔTMD1	constP (0.3)

==Wednesday, September 1 By: Tomonori, Kazuya, Tasuku, Fumitaka, Ken

Making culture and Master plate=

lac rrΔTMD1 constP	many colonies
lac rrΔTMD1 const (control)	many colonies

Screenig PCR of lacP-rrΔTMD1GFP-constP Sample: 1-13 Control: Positive (1-23L) Maker: lambda, 100

   M  1  2  3  4   5  6  7     8  9  10 11 12  13  P M

File:KyotoExp100901.png

Discussion: All of the sample except sample 10 might be self-ligation products of constP.

Miniprep=

rSRRz 1-1	33.8 (ng/µL)
low	56.0 (ng/µL)

Restriction Digestion of rSRRz and low=

Sample name	Template	10xbuffer	100xbuffer	EcoRI	PstI	Water	Total
rSRRz	20	4	0.4	0.3	0.3	15	40
low	20	4	0.4	0.3	0.3	15	40

(13:25-14:30)

Purification=

rSRRz	6.5 (ng/µL)
low	16.8

Ligation and transformation=

Insert: rSRRz 1-1 Vector: low copy plasmid

Thursday, September 2 By: Tomonori, Tomo, Takuya, Ken=

Making culture and Master plate=

rSRRz low	13 colonies
rSRRz low (Control)	13colonies

Screening PCR of rSRRz low=

Sample: rSRRz (1-13) Maker: lambda, 100 Control: Positive (1-23L), Neganive M 1 2 3 4 5 6 7 8 9 10 11 12 13 P N M File:KyotoExp100902.png

Discussion: From sample 1, two vectors might be ligated. Sample 3 and 4, rSRRz might be inserted in low copy plasmid correctly. Sample 11, it might be the self-ligation product of low copy plasmid. Anyway, we decided to culture those 4 colonies on master plate.

Friday, September 3 By: Tomonori, Tomo, Kazuya, Tasuku, Fumitaka, Ken=

Making culture=

lac rrΔTMD1 1, 3 rrΔTMD1 1-1, 1-2 rSRRz 1-1, 1-2 ML

@@ Line 1: / Line 1: @@
 {{:Team:Kyoto/Header}}
 ==Notebook: Construction for Lysisbox==
-===Tuesday, July 20 <span class="by">By: Wataru, Tomo, Yuki, Kazuya, Ken, Makoto</span>===
+==Tuesday, July 20 <span class="by">By: Wataru, Tomo, Yuki, Kazuya, Ken, Makoto</span>===
-====[[Team:Kyoto/Protocols#Transformation|Transformation]]====
+===[[Team:Kyoto/Protocols#Transformation|Transformation]]====
 {| class="experiments"
 !Name||Well||Sample||Competent Cells||Total||Plate||Incubation||Result
@@ Line 25: / Line 25: @@
-===Wednesday, July 21 <span class="by">By: Wataru, Ken, Makoto, Takuya Y.</span>===
+==Wednesday, July 21 <span class="by">By: Wataru, Ken, Makoto, Takuya Y.</span>===
-====Culture at 37&#x2103; from 07/21 20:50 to 07/22 17:00 and Making Master Plate====
+===Culture at 37&#x2103; from 07/21 20:50 to 07/22 17:00 and Making Master Plate====
-====[[Team:Kyoto/Protocols#Transformation|Transformation]]====
+===[[Team:Kyoto/Protocols#Transformation|Transformation]]====
 {| class="experiments"
 !Name||Well||Sample||Competent Cells||Total||Plate||Incubation||Result
@@ Line 35: / Line 35: @@
 |<partinfo>B0015</partinfo>||1-23-L||1||20||21||&#x25CB;
 |}
-====[[Team:Kyoto/Protocols#Stantard PCR|PCR]] for SRRz and S====
+===[[Team:Kyoto/Protocols#Stantard PCR|PCR]] for SRRz and S====
 {| class="experiments"
 !No.||Water||MgSO4||dNTPs||10xBuffer||Template DNA||Primer Fwd.||Primer Rev. (SRRz)||Primer Rev. (S)||KOD Plus ver.2||Total
@@ Line 69: / Line 69: @@
-===Thursday, July 22 <span class="by">By: Wataru</span>===
+==Thursday, July 22 <span class="by">By: Wataru</span>===
-====[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] (40min) of the PCR Products====
+===[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] (40min) of the PCR Products====
 [[Image:KyotoExp100722-1.png|300px|right]]
 {| class="electrophoresis"
@@ Line 92: / Line 92: @@
 |}
 Marker: 100bp, 1kb, 1kb, 100bp.
-====[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
+===[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
 {| class="experiments"
 !Name||Concentration
@@ Line 109: / Line 109: @@
 |}
 The concentration of all samples was very week. Probably our shaking incubation was week.
-====Culture from 07/22 17:00 to 07/23 10:00 and Making Master Plates of <partinfo>pSB4K5</partinfo> and <partinfo>B0015</partinfo>====
+===Culture from 07/22 17:00 to 07/23 10:00 and Making Master Plates of <partinfo>pSB4K5</partinfo> and <partinfo>B0015</partinfo>====
-===Friday, July 23 <span class="by">By: Wataru, Tomo, Makoto</span>===
+==Friday, July 23 <span class="by">By: Wataru, Tomo, Makoto</span>===
-====[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
+===[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
 {| class="experiments"
 !Name||Concentration
@@ Line 122: / Line 122: @@
 |}
 We lost <partinfo>B0015</partinfo> by our mistake. The concentration of <partinfo>pSB4K5</partinfo> is high, so this condition of shaking incubation is moderate.
-====[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]====
+===[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]====
 {| class="experiments"
 !No.||Name||Concentration||New Name
@@ Line 135: / Line 135: @@
 |}
 The concentration of sample number 1 and 5, the PCR products of S-R-Rz/Rz1, is week, so we desided to retry PCR.
-====[[Team:Kyoto/Protocols#Standard_PCR|Standard PCR]] for SRRz====
+===[[Team:Kyoto/Protocols#Standard_PCR|Standard PCR]] for SRRz====
 {| class="experiments"
 !No.||Water||MgSO4||dNTPs||10xBuffer||Template DNA||Primer Fwd. (SRRz)||Primer Rev. (SRRz)||KOD plus ver.2||Total
@@ Line 163: / Line 163: @@
 |4&#x2103;||forever||
 |}
-====[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]] and [[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] (35min) to check function of our Restriction Enzyme====
+===[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]] and [[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] (35min) to check function of our Restriction Enzyme====
 {| class="experiments"
 !No.||Name||Sample||10xBuffer||BSA||colspan="2"|Enzyme||MilliQ||Total||Incubation
@@ Line 180: / Line 180: @@
 Marker: 1kb.
 Comparison to No. 5 (control, circular DNA), the bands of No. 1, 2, 3, and 4 was shifted. The DNA of them was linearized by Restriction enzymes.  So, our restriction enzymes work correctly.
-====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] and [[Team:Kyoto/Protocols#Ligation|Ligation]] to insert S gene to <partinfo>E0840</partinfo>====
+===[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] and [[Team:Kyoto/Protocols#Ligation|Ligation]] to insert S gene to <partinfo>E0840</partinfo>====
 {| class="experiments"
 !Name||Sample||10xBuffer||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total||Incubation
@@ Line 200: / Line 200: @@
-===Monday, July 26 <span class="by">By: Wataru, Tomonori, Makoto</span>===
+==Monday, July 26 <span class="by">By: Wataru, Tomonori, Makoto</span>===
-====[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] of PCR Products====
+===[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] of PCR Products====
 [[Image:KyotoExp100726-1.png|300px|right]]
 {| class="electrophoresis"
@@ Line 220: / Line 220: @@
 Marker: 1kb.
 At the condition 4 (4.5&micro;l MgSO4) and 6 (6&micro;l MgSO4), SRRz is amplified very much. So we decided to use them.
-====PCR Purification====
+===PCR Purification====
 {| class="experiments"
 !No.||Name||Concentration||New Name
@@ Line 230: / Line 230: @@
 |6||SRRZ||59.6||SRRz<sub>Sam7</sub>(2)
 |}
-====[[Team:Kyoto/Protocols#Transformation|Transformation]]====
+===[[Team:Kyoto/Protocols#Transformation|Transformation]]====
 {| class="experiments"
 !Name||Well||Sample||Competent Cell||Total||Plate||Incubation||Result
@@ Line 240: / Line 240: @@
 |<partinfo>J04450</partinfo>||1-5-E||1||20||21||&#xD7;
 |}
-====Culture of <partinfo>pSB4K5</partinfo>, <partinfo>E0840</partinfo>, and <partinfo>B0015</partinfo>====
+===Culture of <partinfo>pSB4K5</partinfo>, <partinfo>E0840</partinfo>, and <partinfo>B0015</partinfo>====
-===Tuesday, July 27 <span class="by">By: Wataru, Tomo, Kazuya, Ken, Naoi===
+==Tuesday, July 27 <span class="by">By: Wataru, Tomo, Kazuya, Ken, Naoi===
-====[[Team:Kyoto/Protocols#Colony PCR|Colony PCR]] of S<sub>Sam7</sub>-E0840 (Electrophoresis for 35min)====
+===[[Team:Kyoto/Protocols#Colony PCR|Colony PCR]] of S<sub>Sam7</sub>-E0840 (Electrophoresis for 35min)====
 [[Image:KyotoExp100727-1.png|300px|right]]
 {| class="electrophoresis"
@@ Line 280: / Line 280: @@
 |}
 Marker: 1kb, 100bp
-====[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
+===[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
 {| class="experiments"
 !Name||Concentration
@@ Line 290: / Line 290: @@
 |<partinfo>E0840</partinfo>||120.1
 |}
-====[[Team:Kyoto/Protocols#RestrictionDigestion|Restriction Digestion]]====
+===[[Team:Kyoto/Protocols#RestrictionDigestion|Restriction Digestion]]====
 {|class="experiments"
 !||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total||Incubation
@@ Line 300: / Line 300: @@
 |SRRz<sub>Sam7</sub>(2)||40||5||0.5||EcoRI||0.4||SpeI||0.4||3.8||50
 |}
-====[[Team:Kyoto/Protocols#Ligation|Ligation]]====
+===[[Team:Kyoto/Protocols#Ligation|Ligation]]====
-====[[Team:Kyoto/Protocols#Transformation|Transformation]]====
+===[[Team:Kyoto/Protocols#Transformation|Transformation]]====
 {| class="experiments"
 !Name||Sample||Competent Cells||Total||Plate||Incubation||Result
@@ Line 311: / Line 311: @@
-===Wednesday, July 28 <span class="by">By: </span>===
+==Wednesday, July 28 <span class="by">By: </span>===
-====[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
+===[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
 {| class="experiments"
 !Name||Concentration
@@ Line 321: / Line 321: @@
 |}
 Diluted S<sub>Sam7</sub>(1)-E0840 and S<sub>Sam7</sub>(2)-E0840 20 times with water, and used as template DNA.
-====[[Team:Kyoto/Protocols#Mutagenesis (Point mutation, Deletion, Insertion)|Deletion PCR]] to delete a functional domain of S gene====
+===[[Team:Kyoto/Protocols#Mutagenesis (Point mutation, Deletion, Insertion)|Deletion PCR]] to delete a functional domain of S gene====
 {| class="experiments"
 !||Water||MgSO4||dNTPs||10xBuffer||Primer Fwd.||Primer Rev.||S<sub>Sam7</sub>(1)-E0840||S<sub>Sam7</sub>(2)-E0840||KOD Plus ver.2||Total
@@ Line 344: / Line 344: @@
 |4&#x2103;||forever||
 |}
-====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] to check the function of DpnI====
+===[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] to check the function of DpnI====
 {| class="experiments"
 !Name||Sample||fast digestion buffer||DpnI||MilliQ||Total
@@ Line 352: / Line 352: @@
 |S<sub>Sam7,&Delta;TMD1</sub>(2)-E0840 (2)||3||1||0.1||5.8||10
 |}
-====[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] for 35min====
+===[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] for 35min====
 [[image:KyotoExp100728-1.png|300px|right]]
 {| class="electrophoresis"
@@ Line 369: / Line 369: @@
-===Thursday, July 29 <span class="by">By: </span>===
+==Thursday, July 29 <span class="by">By: </span>===
-====[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]]====
+===[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]]====
 {| class="experiments"
 !Name||Sample volume||Fastdigestion Buffer||colspan="2"|Enzyme 1||MilliQ||Total||Incubation
@@ Line 378: / Line 378: @@
 |S<sub>Sam7,&Delta;TMD1</sub>(2)-E0840 (1)||50||6||DpnI||0.2||3.8||60
 |}
-====[[Team:Kyoto/Protocols#Ligation|Ligation]] and [[Team:Kyoto/Protocols#Phosphorylation|Phosphorylation]]====
+===[[Team:Kyoto/Protocols#Ligation|Ligation]] and [[Team:Kyoto/Protocols#Phosphorylation|Phosphorylation]]====
 {| class="experiments"
 !Name||Sample||MilliQ||Ligation High||T4 Kinase||Total||Incubation
@@ Line 386: / Line 386: @@
 |S<sub>Sam7,&Delta;TMD1</sub>(1)-E0840 (2)||2||7||5||1||15
 |}
-====[[Team:Kyoto/Protocols#Transformation|Transformation]]====
+===[[Team:Kyoto/Protocols#Transformation|Transformation]]====
 {| class="experiments"
 !Name||Sample Volume||Competent Cell||Total||Plate||Incubation||Result
@@ Line 396: / Line 396: @@
-===Monday, August 2 <span class="by">By: Wataru, Ken</span>===
+==Monday, August 2 <span class="by">By: Wataru, Ken</span>===
-====[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
+===[[Team:Kyoto/Protocols#Miniprep|Miniprep]]====
 {|class="experiments"
 !Name||Concentration(ng/&micro;L)
@@ Line 411: / Line 411: @@
 |<partinfo>R0011</partinfo>||18.6
 |}
-====[[Team:Kyoto/Protocols#Standard_PCR|Standard PCR]] of <partinfo>E0240</partinfo>====
+===[[Team:Kyoto/Protocols#Standard_PCR|Standard PCR]] of <partinfo>E0240</partinfo>====
 E240 is very important parts to measure RPU of promoters in iGEM. However, we failed to transfect it to E.coli from parts kit of iGEM. So we decided to amplify this parts by PCR.
 {|class="experiments"
@@ Line 431: / Line 431: @@
 |4&#x2103;||forever||
 |}
-====[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]]====
+===[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]]====
-====PCR Purification====
+===PCR Purification====
 {|class="experiments"
 !Sample number||Concentration(ng/&micro;L)
@@ Line 440: / Line 440: @@
 |E0240<sub>2</sub>||55.3
 |}
-====[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]] for inserting <partinfo>E0240</partinfo> to pSB4K5 by 3A assembly====
+===[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]] for inserting <partinfo>E0240</partinfo> to pSB4K5 by 3A assembly====
 {| class="experiments"
 !Name||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
@@ Line 448: / Line 448: @@
 |E0240<sub>2</sub>(X-P)||30||5||0.5||XbaI||0.2||PstI||0.2||14.1||50
 |}
-====PCR Purification====
+===PCR Purification====
 {| class="experiments"
 !Name||Concentration(ng/&micro;L)||Volume(&micro;L)
@@ Line 457: / Line 457: @@
 |}
 Stored at -20&#x2103;.
-====Error PCR====
+===Error PCR====
 {|class="experiments"
 !Name||Water||25mM MgSO4||2mM dNTPs||10xBuffer for KOD Plus ver.2||Primer VF2(10&micro;M)||Primer VR(10&micro;M)||Template &Delta;1||Template||Template||KOD Pllus ver.2||Total
@@ Line 476: / Line 476: @@
 |4&#x2103;||forever||
 |}
-====[[Team:Kyoto/Protocols#Transformation|Transformation]]====
+===[[Team:Kyoto/Protocols#Transformation|Transformation]]====
 {| class="experiments"
 !Name||Sample (&micro;l)||Competent Cells (&micro;l)||Total (&micro;l)||Plate||Incubation||Result
@@ Line 488: / Line 488: @@
-===Tuesday, August 3 <span class="by">By: </span>===
+==Tuesday, August 3 <span class="by">By: </span>===
-====Culture of each two colonies of S<sub>&Delta;TMD1</sub>-E0840<sub>1</sub>-1 and S<sub>&Delta;TMD1</sub>-E0840<sub>2</sub> for 37&#x2103; 08/03-08/04====
+===Culture of each two colonies of S<sub>&Delta;TMD1</sub>-E0840<sub>1</sub>-1 and S<sub>&Delta;TMD1</sub>-E0840<sub>2</sub> for 37&#x2103; 08/03-08/04====
-====[[Team:Kyoto/Protocols#Miniprep|Miniprep]] for Construction of Measure(''lac''P) and Measure(Standard)====
+===[[Team:Kyoto/Protocols#Miniprep|Miniprep]] for Construction of Measure(''lac''P) and Measure(Standard)====
 {|class="experiments"
 !Sample number||Concentration(ng/&micro;L)
@@ Line 498: / Line 498: @@
 |<partinfo>R0011</partinfo>||26.8
 |}
-====[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]]====
+===[[Team:Kyoto/Protocols#Restriction_Digestion|Restriction Digestion]]====
 {|class="experiments"
 !Name||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
@@ Line 510: / Line 510: @@
 |E0240<sub>2</sub>(X-P)||50||6||0.6||XbaI||0.2||PstI||0.2||3||60
 |}
-====PCR Purification====
+===PCR Purification====
 {|class="experiments"
 !Sample number||Concentration(ng/&micro;L)
@@ Line 521: / Line 521: @@
 |}
 pSB4K5(E-P) is concentrated 10&micro;L and E0240<sub>1</sub>(X-P), E0240<sub>2</sub>(X-P) are concentrated 1&micro;L.
-====Ethanol Precipitation====
+===Ethanol Precipitation====
-====Dilution of <partinfo>pSB4K5</partinfo> by 2&micro;l MilliQ====
+===Dilution of <partinfo>pSB4K5</partinfo> by 2&micro;l MilliQ====
-====[[Team:Kyoto/Protocols#Ligation|Ligation]]====
+===[[Team:Kyoto/Protocols#Ligation|Ligation]]====
 {|class="experiments"
 !||Vector||colspan="2"|Insert 1||colspan="2"|Insert 2||Ligation High||Total||Incubation
@@ Line 531: / Line 531: @@
 |R0011-E0240<sub>2</sub>[Low]||pSB4K5(E-P)||1||R0011(E-S)||1||E0240<sub>2</sub>(X-P)||1||3||15
 |}
-====[[Team:Kyoto/Protocols#Standard PCR|Standard PCR]] of <partinfo>J23101</partinfo>-<partinfo>E0240</partinfo> that is important in the measurement of RPU====
+===[[Team:Kyoto/Protocols#Standard PCR|Standard PCR]] of <partinfo>J23101</partinfo>-<partinfo>E0240</partinfo> that is important in the measurement of RPU====
 {|class="experiments"
 !Name||Water||25mM MgSO4||2mM dNTPs||10xBuffer for KOD Plus ver.2||Primer VF2(10&micro;M)||Primer VR(10&micro;M)||Template J23101-E0240||KOD plus ver.2	||Total
@@ Line 550: / Line 550: @@
 |4&#x2103;||forever||
 |}
-====[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]====
+===[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]====
 {|class="experiments"
 !Name||Concentration(ng/&micro;L)
@@ Line 556: / Line 556: @@
 |J23101-E0240||40.6
 |}
-====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]]====
+===[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]]====
 {|class="experiments"
 !Name||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
@@ Line 562: / Line 562: @@
 |J23101-E0240(E-P)||45||6||0.6||EcoRI||0.2||PstI||0.2||8||60
 |}
-====[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]====
+===[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]====
 {| class="experiments"
 !Name||Concentration(ng/&micro;L)||Volume(&micro;L)
@@ Line 569: / Line 569: @@
 |}
 J23101-E0240(E-P) is concentrated 7&micro;L
-====[[Team:Kyoto/Protocols#Ligation|Ligation]]====
+===[[Team:Kyoto/Protocols#Ligation|Ligation]]====
 {|class="experiments"
 !||Vector||colspan="2"|Insert||colspan="2"|Ligation High||Total||Incubation
@@ Line 576: / Line 576: @@
 |}
 <div class="measure-construction"><br />
-====Transformation====
+===Transformation====
 {| class="experiments"
 !Name||Conc(/&micro;L)||Sample Volume(&micro;L)||Competent Cell(&micro;L)||Total||Plate||Incubation
@@ Line 588: / Line 588: @@
-===Thursday, August 5 <span class="by">By: </span>===
+==Thursday, August 5 <span class="by">By: </span>===
-====Result of Transformation====
+===Result of Transformation====
 {|class="experiments"
 |R0011-E0240<sub>1</sub>[Low]||rowspan="3"|Many colonies
@@ Line 639: / Line 639: @@
-===Friday, August 6===
+==Friday, August 6===
-====Miniprep====
+===Miniprep====
 {| class="experiments"
 !Name
@@ Line 666: / Line 666: @@
 |J23101-E0240[Low]-3
 |}
-====Restriction Digestion====
+===Restriction Digestion====
 {|class="experiments"
 !Name||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
@@ Line 730: / Line 730: @@
 [[Image:KyotoExp100806-1.png]]
 White colonies are not inserted <partinfo>R0011</partinfo> but its vector. Top10 we used are deleted Lac operon. Then, correctly inserted parts is green because of the lack of ''lacI'' gene.
-====Error PCR (Retry)====
+===Error PCR (Retry)====
 {| class="experiments"
 !Name||Water||25mM MgSO4||2mM dNTPs||10xBuffer for KOD Plus ver.2||Primer VF2(10&micro;M)||Primer VR(10&micro;M)||Template &Delta;TMD failed(50ng/&micro;L)||KOD plus ver.2||Total
@@ Line 751: / Line 751: @@
 |4&#x2103;||forever||
 |}
-====Transformation====
+===Transformation====
 {| class="experiments"
 !Name||Conc(/&micro;L)||Sample Volum(&micro;L)||Competent Cell(&micro;L)||Total||Plate||Incubation
@@ Line 765: / Line 765: @@
-===Monday, August 9 <span class="by">By: Wataru, Tomonori, Ken, Takuya</span>===
+==Monday, August 9 <span class="by">By: Wataru, Tomonori, Ken, Takuya</span>===
-====Miniprep of MS and ML====
+===Miniprep of MS and ML====
 {|class="experiments"
 !Sample number||concentration(ng/&micro;L)
@@ Line 774: / Line 774: @@
 |ML||146.6
 |}
-====Transfotrmation of MS and ML====
+===Transfotrmation of MS and ML====
 {|class="experiments"
 !Sample||conc(ng/&micro;L)||Sample vol(&micro;L)||Competent Cell||Competent cell vol(&micro;L)||Total vol(&micro;L)||Plate||Incuvation
@@ Line 782: / Line 782: @@
 |ML||146.6||2||KRX||50||52
 |}
-====Restriction enzyme digestion and ethanol precipitation====
+===Restriction enzyme digestion and ethanol precipitation====
 To use lac p for next ligation, we digested 1-6-G by EroRI and PstI
 {|class="experiments"
@@ Line 791: / Line 791: @@
 Incubate 37&#x2103; 8/9 16:20‾18:20
 After restriction enzyme digestion, we did ethanol precipitation.
-====Ligation and Transformation====
+===Ligation and Transformation====
 {|class="experiments"
 !Sample||Conc (nu/&micro;L)||Sample vol (&micro;L)||Competent cell||Competent cell vol (&micro;L)||Total vol (&micro;L)||Plate||Incuvation
@@ Line 801: / Line 801: @@
-===Tuesday, August 10 <span class="by">By: Wataru, Tomonori, Ken, Fumitaka</span>
+==Tuesday, August 10 <span class="by">By: Wataru, Tomonori, Ken, Fumitaka</span>
-====Making culture plate on lac p (low), MS and ML====
+===Making culture plate on lac p (low), MS and ML====
 {|class="experiments"
 |rowspan="2"|Lac p (low)||KRX||rowspan="4"|Many colonies
@@ Line 812: / Line 812: @@
 |ML||KRX
 |}
-====Minprep of &Delta;TMD1+GFP====
+===Minprep of &Delta;TMD1+GFP====
 {|class="experiments"
 !Sample number||Concentration (ng/&micro;L)
@@ Line 825: / Line 825: @@
 |}
 &#x2103; 8/9 18:00‾8/10 9:00
-====Culture and Master Plate====
+===Culture and Master Plate====
-===Wednesday, August 11 <span class="by">By: Wataru, Naoi, Ken, Takuya</span>
+==Wednesday, August 11 <span class="by">By: Wataru, Naoi, Ken, Takuya</span>
 {| class="experiments"
 !Sample||Medium||Cloud||Incubation
@@ Line 861: / Line 861: @@
 |}
 Discussion: About sample 1, 3, 4, 5 and 7, lac promoter was correctly inserted in low copy plasmid. About sample 2 and 6, low copy plasmid and vector derived from lac promoter were ligated. We decided to use sample 1 or 3.
-====Miniprep of C2+lac(low), S-R-Rz 1', 3'====
+===Miniprep of C2+lac(low), S-R-Rz 1', 3'====
 lac(low)1	: 31.2 (ng/&micro;L)
 lac(low)2	: 29.9 (ng/&micro;L)
-====Restriction Digestion and electrophoresis of lac (low) 1 and 3====
+===Restriction Digestion and electrophoresis of lac (low) 1 and 3====
 {| class="experiments"
 !Name||EcoRI||PstI
@@ Line 880: / Line 880: @@
 [[image:KyotoExp100811-1.png]]
 Discussion: Each enzyme correctly cut samples.
-====Screening PCR of SRRz====
+===Screening PCR of SRRz====
 Sample: 1-20
 Control: P(1-23L) P'(2-8E) N
@@ Line 891: / Line 891: @@
-===Thursday, August 12 <span class="by">By: Wataru, Ken</span>===
+==Thursday, August 12 <span class="by">By: Wataru, Ken</span>===
-====Restriction Digestion and electrophoresis of <partinfo>B0015</partinfo>====
+===Restriction Digestion and electrophoresis of <partinfo>B0015</partinfo>====
 {| class="experiments"
 !Sample name||Template||10xbuffer||100xbuffer||EcoRI||XbaI 1||XbaI 2||SpeI||PstI 1||PstI 2||Water||Total
@@ Line 916: / Line 916: @@
-===Thursday, August 19 <span class="by">By: Wataru, Tomo, Ken</span>
+==Thursday, August 19 <span class="by">By: Wataru, Tomo, Ken</span>
-====Miniprep of S&Delta;TMD1GFP====
+===Miniprep of S&Delta;TMD1GFP====
 .6(ng/&micro;g)
-====Point mutation PCR of &Delta;TMD1GFP====
+===Point mutation PCR of &Delta;TMD1GFP====
 {| class="experiments"
 !Sample number||Template||10xbuffer||dNTPs||MgSO4||Primer 1||Primer 2||Water||KOD-plus-||Total
@@ Line 940: / Line 940: @@
 |4.0||forever||
 |}
-====Restriction Digestion(DpnI): 17:50-18:50====
+===Restriction Digestion(DpnI): 17:50-18:50====
-====Electrophoresis====
+===Electrophoresis====
 Sample: 1, 2, Control Marker: lambda, 100
 [[Image:KyotoExp100819-1.png]]
-====Ligation and Transformation====
+===Ligation and Transformation====
 We named point mutation PCR products r&Delta;TMD1GFP.
-===Monday, August 23 <span class="by">By: Wataru, Tomo, Ken, Fumitaka, Tasuku</span>===
+==Monday, August 23 <span class="by">By: Wataru, Tomo, Ken, Fumitaka, Tasuku</span>===
-====Miniprep of &Delta;TMD1====
+===Miniprep of &Delta;TMD1====
 {| class="experiments"
 |Sample number||Concentration(ng/&micro;g)
@@ Line 957: / Line 957: @@
 |2-2||49.9
 |}
-====Sequencing of &Delta;TMD1 and MS====
+===Sequencing of &Delta;TMD1 and MS====
 Sample: r&delta;TMD1GFP1-1, 2-2, and MS
 Discussion: The sequencing was in success and the results were desirable. It meant point mutation of &delta;TMD1GFP was succeeded and sequence of MS was confirmed. We decided to use r&delta;TMD1GFP.
-====Screening PCR of SRRz-DT====
+===Screening PCR of SRRz-DT====
 Sample: 1-13, Marker: lambda and 100, Control:P(1-23L) and N
 {| class="experiments"
@@ Line 978: / Line 978: @@
 [[Image:KyotoExp100823-1.png]]
 Discussion: We found the band; about 200bp, and it meant the lligation was completed successfully.
-====Deletion PCR of r&Delta;TMD1GFP 2-2====
+===Deletion PCR of r&Delta;TMD1GFP 2-2====
 {| class="experiments"
 !Sample||10x||dNTPs||Primer1||Primer2||Template||Water||KOD-plus-||Total
@@ Line 999: / Line 999: @@
 |4&#x2103;||hold||
 |}
-====Restriction Digestion(DpnI)====
+===Restriction Digestion(DpnI)====
 {| class="experiments"
 |Template||25(&micro;L)
@@ Line 1,008: / Line 1,008: @@
 |}
 :10-20:10
-====Ligation====
+===Ligation====
 {|class="experiments"
 !Sample||Template||Water||Ligation high||T4 Kinase||total
@@ Line 1,019: / Line 1,019: @@
 |}
 :15-21:15
-====Transformation====
+===Transformation====
 We named sample 1, 2 and control rr&delta;TMD1GFP1, 2 and control.
-===Tuesday, August 24 <span class="by">By:Ken, Tomo, Tasuku, Takuya</span>===
+==Tuesday, August 24 <span class="by">By:Ken, Tomo, Tasuku, Takuya</span>===
-====Retry of deletion PCR of r&delta;TMD1 GFP====
+===Retry of deletion PCR of r&delta;TMD1 GFP====
 {| class="experiments"
 !Sample||10x||dNTPs||MgSO4||Primer1||Primer2||Template||Water||KOD-plus-||Total
@@ Line 1,045: / Line 1,045: @@
 |4&#x2103;||hold||
 |}
-====Restriction Digestion (DpnI)====
+===Restriction Digestion (DpnI)====
 :15-15:15
-====Electrophoreis====
+===Electrophoreis====
 Sample: 1, 2, and control, Maker: 100 and lambda
 M    1   2   C        M
 [[Image:KyotoExp100824-1.png]]
 We found the band of sample 1 and 2 about 3000bp and there wasn't the band of sample control. So, we confirmed the PCR and RE were completed successfully.
-====Ligation====
+===Ligation====
-====Point mutation of SRRz====
+===Point mutation of SRRz====
 {| class="experiments"
 !Sample||10x||dNTPs||MgSO4||Primer1||Primer2||Template||Water||KOD-plus-||total
@@ Line 1,075: / Line 1,075: @@
 |4&#x2103;||hold||
 |}
-====Restriction Digestion(DpnI), electrophoresis and ligation====
+===Restriction Digestion(DpnI), electrophoresis and ligation====
 [[Image:KyotoExp100824-2.png]]
 We could find point mutation PCR and restriction enzyme of DpnI was done.
-===PCR of E0240===
+==PCR of E0240===
 {| class="experiments"
 !Sample||10&#x7D;||dNTPs||MgSO4||VF2||VR||Template||Water||KOD-plus-||Total
@@ Line 1,091: / Line 1,091: @@
-===PCR Purification===
+==PCR Purification===
 Sample1: 5.5*50(ng/&micro;L)
 Sample2: 5.2*50(ng/&micro;L)
-====Restriction Digestion(EcoRI, PstI) and Gel extraction====
+===Restriction Digestion(EcoRI, PstI) and Gel extraction====
 Sample1: 28.8 (ng/&micro;L)
 Sample2: 26.4 (ng/&micro;L)
-====Transformation====
+===Transformation====
 Sample: rr&Delta;TMD1GFP1. 2. control, and rSRRz1. 2. control
-===Wednesday, August 25 <span class="by">By:Ken, Tomo, Kazuya, Tasuku, Takuya<span>===
+==Wednesday, August 25 <span class="by">By:Ken, Tomo, Kazuya, Tasuku, Takuya<span>===
-====Making culture and Master plate====
+===Making culture and Master plate====
 {| class="experiments"
 |rr&Delta;TMD1-1||rowspan="2"|Many Colonies
@@ Line 1,116: / Line 1,116: @@
 |rSRRz-C-||zero
 |}
-====Miniprep of 1-5G====
+===Miniprep of 1-5G====
 .0 (ng/&micro;L)
-====Restriction Digestion and purification of 1-5G(low copy plasmid) and lac low====
+===Restriction Digestion and purification of 1-5G(low copy plasmid) and lac low====
 {| class="experiments"
 !Sample name||Template||10xbuffer||100xbuffer||EcoRI||SpeI||PstI||Water||Total
@@ Line 1,133: / Line 1,133: @@
 |Lac low||8.6
 |}
-====Ligation of <partinfo>E0240</partinfo> and <partinfo>pSB4K5</partinfo>, Transformation====
+===Ligation of <partinfo>E0240</partinfo> and <partinfo>pSB4K5</partinfo>, Transformation====
-===Thursday, August 26 <span class="by">By:Ken, Tomo, Kazuya, Tasuku, Takuya, Fumitaka</span>
+==Thursday, August 26 <span class="by">By:Ken, Tomo, Kazuya, Tasuku, Takuya, Fumitaka</span>
-====Miniprep====
+===Miniprep====
 {| class="experiments"
 |Sample name||Concentration(ng/&micro;L)
@@ Line 1,143: / Line 1,143: @@
 |constP(0.7)||44.5
 |}
-====Restriction Digestion of constP(0.7)====
+===Restriction Digestion of constP(0.7)====
 {| class="experiments"
 !Template||10xbuffer||100xbuffer||SpeI||PstI||Water||Total
@@ Line 1,149: / Line 1,149: @@
 |25||4||0.4||0.3||0.3||10||40
 |}
-====Purification of constP (0.7)====
+===Purification of constP (0.7)====
 .8 ng/&micro;L
-===Friday, August 27 <span class="by">By:Ken, Tomo, Kazuya, Fumitaka</span>===
+==Friday, August 27 <span class="by">By:Ken, Tomo, Kazuya, Fumitaka</span>===
-====Making master plate of E0240 low====
+===Making master plate of E0240 low====
 {| class="experiments"
 |Sample Name||Concentration(ng/&micro;L)
@@ Line 1,162: / Line 1,162: @@
 |rSRRz 1-1||16.4
 |}
-====Restriction Digestion of rr&Delta;TMD1 and rSRRz====
+===Restriction Digestion of rr&Delta;TMD1 and rSRRz====
 {| class="experiments"
 !Sample name||Template||10xbuffer||100xbuffer||XbaI||PstI||Water||Total
@@ Line 1,171: / Line 1,171: @@
 |}
 (13:20-14:20)
-====Purification====
+===Purification====
 {|Sample Name||Concentration(ng/&micro;L)
 |-
@@ Line 1,178: / Line 1,178: @@
 |rSRRz 1-1||56.1
 |}
-====Lagation and transformation====
+===Lagation and transformation====
 lacP + rr&Delta;TMD1 1-2
 constP (0.7) + rr&Delta;TMD1 1-2
@@ Line 1,184: / Line 1,184: @@
-===Monday, August 30 <span class="by">By: Tomonori, Kazuya, Tasuku, Ken</span>===
+==Monday, August 30 <span class="by">By: Tomonori, Kazuya, Tasuku, Ken</span>===
-====Making culture and Master plate====
+===Making culture and Master plate====
 {|class="experiments"
 |lacP rr&Delta;TMD1GFP||Many colonies
@@ Line 1,203: / Line 1,203: @@
-===Tuesday, August 31 <span class="by">By: Tomonori, Takuya Y., Kazuya, Tasuku, Takuya, Ken<span>
+==Tuesday, August 31 <span class="by">By: Tomonori, Takuya Y., Kazuya, Tasuku, Takuya, Ken<span>
-====Miniprep====
+===Miniprep====
 {|class="experiments"
 |constP (0.3)||48.5 (ng/&micro;L)
@@ Line 1,210: / Line 1,210: @@
 |lac rr&Delta;TMD1||107.3
 |}
-====RE of constP (0.3) and lac rr&Delta;TMD1====
+===RE of constP (0.3) and lac rr&Delta;TMD1====
-====Gel Extraction of lac rr&Delta;TMD1====
+===Gel Extraction of lac rr&Delta;TMD1====
 [[image:KyotoExp100831-1.png]]
 min
 Discussion: There were two band at the bottom of the gel.  It was too long -45min-, and insert and vector might be contaminated.  But we went on next operation.
-====Purification of constP (0.3) and lac rr&Delta;TMD1====
+===Purification of constP (0.3) and lac rr&Delta;TMD1====
 {|class="experiments"
 |constP (0.3)||5.8 (ng/&micro;L)
@@ Line 1,222: / Line 1,222: @@
 |lac rr&Delta;TMD1||7.8 (ng/&micro;L)
 |}
-====Ligation and transformation====
+===Ligation and transformation====
 {|class="experiments"
 |Insert||Vector
@@ Line 1,230: / Line 1,230: @@
-===Wednesday, September 1 <span class="by">By: Tomonori, Kazuya, Tasuku, Fumitaka, Ken</span>
+==Wednesday, September 1 <span class="by">By: Tomonori, Kazuya, Tasuku, Fumitaka, Ken</span>
-====Making culture and Master plate====
+===Making culture and Master plate====
 {| class="experiments"
 |lac rr&Delta;TMD1 constP||many colonies
@@ Line 1,243: / Line 1,243: @@
 Discussion: All of the sample except sample 10 might be self-ligation products of constP.
-====Miniprep====
+===Miniprep====
 {|class="experiments"
 |rSRRz 1-1||33.8 (ng/&micro;L)
@@ Line 1,249: / Line 1,249: @@
 |low||56.0 (ng/&micro;L)
 |}
-====Restriction Digestion of rSRRz and low====
+===Restriction Digestion of rSRRz and low====
 {|class="experiments"
 !Sample name||Template||10xbuffer||100xbuffer||EcoRI||PstI||Water||Total
@@ Line 1,258: / Line 1,258: @@
 |}
 (13:25-14:30)
-====Purification====
+===Purification====
 {|class="experiments"
 |rSRRz||6.5 (ng/&micro;L)
@@ Line 1,264: / Line 1,264: @@
 |low||16.8
 |}
-====Ligation and transformation====
+===Ligation and transformation====
 	Insert: rSRRz 1-1	Vector: low copy plasmid
-===Thursday, September 2 <span class="by">By: Tomonori, Tomo, Takuya, Ken<span>===
+==Thursday, September 2 <span class="by">By: Tomonori, Tomo, Takuya, Ken<span>===
-====Making culture and Master plate====
+===Making culture and Master plate====
 {|class="experiments"
 |rSRRz low||13 colonies
@@ Line 1,275: / Line 1,275: @@
 |rSRRz low (Control)||13colonies
 |}
-====Screening PCR of rSRRz low====
+===Screening PCR of rSRRz low====
 Sample: rSRRz (1-13)
 Maker: lambda, 100
@@ Line 1,285: / Line 1,285: @@
-===Friday, September 3 <span class="by">By: Tomonori, Tomo, Kazuya, Tasuku, Fumitaka, Ken</span>===
+==Friday, September 3 <span class="by">By: Tomonori, Tomo, Kazuya, Tasuku, Fumitaka, Ken</span>===
-====Making culture====
+===Making culture====
 lac rr&Delta;TMD1 1, 3
 rr&Delta;TMD1 1-1, 1-2

Sample name	Template	10xbuffer	100xbuffer	EcoRI	XbaI 1	XbaI 2	SpeI	PstI 1	PstI 2	Water	Total
1	3	1	0.1	0.2	-	-	-	-	-	5.7	10
2	3	1	0.1	-	0.2	-	-	-	-	5.7	10
3	3	1	0.1	-	-	0.2	-	-	-	5.7	10
4	3	1	0.1	-	-	-	0.2	-	-	5.7	10
5	3	1	0.1	-	-	-	-	0.2	-	5.7	10
6	3	1	0.1	-	-	-	-	-	0.2	5.7	10
N	3	1	0.1	-	-	-	-	-	-	5.9	10

Sample name	Template	10xbuffer	100xbuffer	EcoRI	XbaI 1	XbaI 2	SpeI	PstI 1	PstI 2	Water	Total
1	3	1	0.1	0.2	-	-	-	-	-	5.7	10
2	3	1	0.1	-	0.2	-	-	-	-	5.7	10
3	3	1	0.1	-	-	0.2	-	-	-	5.7	10
4	3	1	0.1	-	-	-	0.2	-	-	5.7	10
5	3	1	0.1	-	-	-	-	0.2	-	5.7	10
6	3	1	0.1	-	-	-	-	-	0.2	5.7	10
N	3	1	0.1	-	-	-	-	-	-	5.9	10

Team:Kyoto/Notebook/Construction

From 2010.igem.org

Revision as of 09:13, 17 October 2010

Contents

Notebook: Construction for Lysisbox

Tuesday, July 20 By: Wataru, Tomo, Yuki, Kazuya, Ken, Makoto=

Transformation=

Wednesday, July 21 By: Wataru, Ken, Makoto, Takuya Y.=

Culture at 37℃ from 07/21 20:50 to 07/22 17:00 and Making Master Plate=

Transformation=

PCR for SRRz and S=

Thursday, July 22 By: Wataru=

Electrophoresis (40min) of the PCR Products=

Miniprep=

Culture from 07/22 17:00 to 07/23 10:00 and Making Master Plates of <partinfo>pSB4K5</partinfo> and <partinfo>B0015</partinfo>=

Friday, July 23 By: Wataru, Tomo, Makoto=

Miniprep=

PCR Purification=

Standard PCR for SRRz=

Restriction Digestion and Electrophoresis (35min) to check function of our Restriction Enzyme=

Restriction Digestion and Ligation to insert S gene to <partinfo>E0840</partinfo>=

Monday, July 26 By: Wataru, Tomonori, Makoto=

Electrophoresis of PCR Products=

PCR Purification=

Transformation=

Culture of <partinfo>pSB4K5</partinfo>, <partinfo>E0840</partinfo>, and <partinfo>B0015</partinfo>=

Tuesday, July 27 By: Wataru, Tomo, Kazuya, Ken, Naoi=

Colony PCR of SSam7-E0840 (Electrophoresis for 35min)=

Miniprep=

Restriction Digestion=

Ligation=

Transformation=

Wednesday, July 28 By: =

Miniprep=

Deletion PCR to delete a functional domain of S gene=

Restriction Digestion to check the function of DpnI=

Electrophoresis for 35min=

Thursday, July 29 By: =

Restriction Digestion=

Ligation and Phosphorylation=

Transformation=

Monday, August 2 By: Wataru, Ken=

Miniprep=

Standard PCR of <partinfo>E0240</partinfo>=

Electrophoresis=

PCR Purification=

Restriction Digestion for inserting <partinfo>E0240</partinfo> to pSB4K5 by 3A assembly=

PCR Purification=

Error PCR=

Transformation=

Tuesday, August 3 By: =

Culture of each two colonies of SΔTMD1-E08401-1 and SΔTMD1-E08402 for 37℃ 08/03-08/04=

Miniprep for Construction of Measure(lacP) and Measure(Standard)=

Restriction Digestion=

PCR Purification=

Ethanol Precipitation=

Dilution of <partinfo>pSB4K5</partinfo> by 2µl MilliQ=

Ligation=

Standard PCR of <partinfo>J23101</partinfo>-<partinfo>E0240</partinfo> that is important in the measurement of RPU=

PCR Purification=

Restriction Digestion=

PCR Purification=

Ligation=

Transformation=

Thursday, August 5 By: =

Result of Transformation=

Friday, August 6=

Miniprep=

Restriction Digestion=

Electrophoresis

Error PCR (Retry)=

Transformation=

Monday, August 9 By: Wataru, Tomonori, Ken, Takuya=

Miniprep of MS and ML=

Transfotrmation of MS and ML=

Restriction enzyme digestion and ethanol precipitation=

Ligation and Transformation=

Making culture plate on lac p (low), MS and ML=

Minprep of ΔTMD1+GFP=

Culture and Master Plate=

Colony PCR of S_Sam7-E0840 (Electrophoresis for 35min)=

Culture of each two colonies of S_ΔTMD1-E0840₁-1 and S_ΔTMD1-E0840₂ for 37℃ 08/03-08/04=

Sample name	Template	10xbuffer	100xbuffer	EcoRI	XbaI 1	XbaI 2	SpeI	PstI 1	PstI 2	Water	Total
1	3	1	0.1	0.2	-	-	-	-	-	5.7	10
2	3	1	0.1	-	0.2	-	-	-	-	5.7	10
3	3	1	0.1	-	-	0.2	-	-	-	5.7	10
4	3	1	0.1	-	-	-	0.2	-	-	5.7	10
5	3	1	0.1	-	-	-	-	0.2	-	5.7	10
6	3	1	0.1	-	-	-	-	-	0.2	5.7	10
N	3	1	0.1	-	-	-	-	-	-	5.9	10