Team:Kyoto/Notebook1

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Revision as of 12:13, 23 October 2010

LastModified: 2010-10-23

Notebook

Construction for Lysisbox

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

Transformation

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

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

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	Colony
pSB4K5	1-5-G	1 µL	20	21	LB (Kan+)	At 37℃, 7/21 20:50 - 7/22 16:30	○
B0015	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℃	10s	30 cycles
55℃	30s
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
J23100	18.5 (ng/µL)
J23105	12.5
J23116	14.6
R0011	8.6
E0840	12.1
J06702	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 pSB4K5 and B0015

Friday, July 23 By: Wataru, Tomo, Makoto

Miniprep

Name	Concentration
pSB4K5	79.2 (ng/µL)
B0015	-

We lost B0015 by our mistake. The concentration of pSB4K5 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.

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℃	10s	30 cycles
55℃	30s
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	J06702	5 µL	1	0.1	EcoRI	0.1	3.6	10	At 37℃ 7/23 18:00 - 7/23 18:30
2	J06702	5	1	0.1	XbaI	0.1	3.6	10
3	J06702	5	1	0.1	SpeI	0.1	3.6	10
4	J06702	5	1	0.1	PstI	0.1	3.6	10
5	J06702	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 E0840

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
E0840	45	5	EcoRI	0.2	XbaI	0.2	0	50

After PCR Purification, evaporated them and diluted 3µL.

Name	Vector		Insert		Ligation High	Total
S_Sam7(1)-E0840	E0840	0.5µL	S_Sam7(1)	0.5	1	2
S_Sam7(2)-E0840	E0840	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	Colony
E0240	1-12-M	1 µL	20	21	LB (Amp+)	At 37℃ 7/26 - 7/27	×
I20260	2-17-F	1	20	21	LB (Kan+)		×
J04450	1-5-E	1	20	21	LB (Kan+)		×

Culture of pSB4K5, E0840, and B0015

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	○
+	E0840	1116
-	None

Marker: 1kb, 100bp

Miniprep

Name	Concentration
R0011	26.9 ng/µL
B0015	120.0
E0840	120.1

Restriction Digestion

Name	Sample	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total	Incubation
B0015	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	Colony
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.	Template (1)	Template (2)	KOD Plus ver.2	Total
S_Sam7,ΔTMD1(1)-E0840 (1)	28 µL	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℃	10s	35 cycles
55℃	30s
68℃	4min
4℃	forever

Restriction Digestion to check the function of DpnI

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

Electrophoresis for 35min

No.	Name	Length
1	Not digested S_Sam7(1)-E0840	3363bp
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(2)-E0840 (1)	2	7	5	1	15	07/29 11:30 ~ 07/29 13:00

Transformation

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

Monday, August 2 By: Wataru, Ken

Miniprep

Name	Concentration
S_Sam7,ΔTMD1-E0840 (1)	52.7 ng/µL
S_Sam7,ΔTMD1-E0840 (2)	54.4
S_Sam7,ΔTMD1-E0840 (3)	89.5
pSB4K5	50.7
R0011	18.6

Standard PCR of E0240

E0240 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	MgSO4	dNTPs	10xBuffer	Primer VF2	Primer VR	Template E0240	KOD Pllus ver.2	Total
E0240(1)	28 µL	3	5	5	1.5	1.5	5	1	50
E0240(2)	28	3	5	5	1.5	1.5	5	1	50

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

Electrophoresis

PCR Purification

Name	Concentration
E0240(1)	42.6 ng/µL
E0240(2)	55.3

Restriction Digestion for inserting E0240 to pSB4K5 by 3A assembly

Name	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
E0240(1) [XP]	30 µL	5	0.5	XbaI	0.2	PstI	0.2	14.1	50
E0240(2) [XP]	30	5	0.5	XbaI	0.2	PstI	0.2	14.1	50

PCR Purification

Name	Concentration	Volume
E0240(1) [XP]	21.8 ng/µL	40 µL
E0240(2) [XP]	32.4	45

Stored at -20℃.

Error PCR

Name	Water	MgSO4	dNTPs	10xBuffer	Primer VF2	Primer VR	Template (1)	Template (2)	Template (3)	KOD Pllus ver.2	Total
S_Sam7,ΔTMD1-E0840 (1)	32 µL	3	5	5	1.5	1.5	1	-	-	1	50
S_Sam7,ΔTMD1-E0840 (2)	32	3	5	5	1.5	1.5	-	1	-	1	50
S_Sam7,ΔTMD1-E0840 (3)	32	3	5	5	1.5	1.5	-	-	1	1	50

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

Restriction Digestion of S_Sam7,ΔTMD1-E0840 by DpnI

Transformation

Name	Sample	Competent Cells	Total	Plate	Incubation	Colony
S_Sam7,ΔTMD1-E0840 (1)	2 µL	20	22	-	-	○
S_Sam7,ΔTMD1-E0840 (2)	2	20	22			}
S_Sam7,ΔTMD1-E0840 (3)	2	20	22			○

Tuesday, August 3 By:

Culture

Picked two colonies from S_Sam7,ΔTMD1-E0840 (1), and S_Sam7,ΔTMD1-E0840 (3), and cultured at 37℃ from 08/03 to 08/04.

Miniprep

Name	Concentration
pSB4K5	60.7 ng/µL
R0011	26.8

Restriction Digestion

Name	Sample	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
R0011 [ES]	50 µL	6	0.6	EcoRI	0.2	SpeI	0.2	3	60
pSB4K5 [EP]	50	6	0.6	EcoRI	0.2	PstI	0.2	3	60
E0240(1) [XP]	50	6	0.6	XbaI	0.2	PstI	0.2	3	60
E0240(2) [XP]	50	6	0.6	XbaI	0.2	PstI	0.2	3	60

PCR Purification

Name	Concentration
pSB4K5 [EP]	39.5 ng/µL
E0240(1) [XP]	21.8
E0240(2) [XP]	32.4

pSB4K5 [EP] is concentrated 10µL and E0240(1) [XP], E0240(2) [XP] are concentrated 1µL.

Ethanol Precipitation

After ethanol precipitation, we diluted pSB4K5 by 2µL MilliQ

Ligation

Name	Vector	Insert 1		Insert 2		Ligation High	Total	Incubation
R0011-E0240(1) [pSB4K5]	pSB4K5 [EP]	1	R0011 [ES]	1	E0240(1) [XP]	1	3	15	17:30 - 20:20
R0011-E0240(2) [pSB4K5]	pSB4K5 [EP]	1	R0011 [ES]	1	E0240(2) [XP]	1	3	15	17:30 - 20:20

Standard PCR of I20260

Name	Water	MgSO4	dNTPs	10xBuffer	Primer VF2	Primer VR	Template I20260	KOD plus ver.2	Total
I20260 (1)	32µL	3	5	5	1.5	1.5	1	1	50
I20260 (2)	32	3	5	5	1.5	1.5	-	1	50

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

PCR Purification

Name	Concentration
I20260	40.6 ng/µL

Restriction Digestion

Name	Sample volume	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
I20260 [EP]	45 µL	6	0.6	EcoRI	0.2	PstI	0.2	8	60

PCR Purification

Name	Concentration	Volume
I20260 [EP]	74.1 ng/µL	30

I20260 [EP] is concentrated at 7µL

Ligation

	Vector	Insert		Ligation High		Total	Incubation
I20260 [pSB4K5]	pSB4K5 [EP]	1	I20260 [EP]	1	2	4	20:00-20:30

Transformation

Name	Sample	Competent Cell	Total	Plate	Incubation	Colony
R0011-E0240(1) [pSB4K5]	1 µL	20	21	LB (Kan+)	08/03-08/04	○
R0011-E0240(2) [pSB4K5]	1	20	21			○
I20260 [pSB4K5]	1	20	21			○

Thursday, August 5 By:

Culture and Master Plates

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-E0240(1) [pSB4K5] and R0011-E0240(2) [pSB4K5] plate. We cultured both white and green colonies.

In I20260 [pSB4K5], Many of colonies are red, but green colonies are observed. We cultured green colonies.

Name	Color	Incubation
R0011-E0240(1) [pSB4K5] (1)	Green Colony	8/5-8/6
R0011-E0240(1) [pSB4K5] (2)	Green Colony
R0011-E0240(1) [pSB4K5] (3)	White Colony
R0011-E0240(1) [pSB4K5] (4)	White Colony
R0011-E0240(2) [pSB4K5] (1)	Green Colony
R0011-E0240(2) [pSB4K5] (2)	White Colony
R0011-E0240(2) [pSB4K5] (3)	White Colony
R0011-E0240(2) [pSB4K5] (4)	White Colony
I20260 [pSB4K5] (1)	Green Colony
I20260 [pSB4K5] (2)	Green Colony
I20260 [pSB4K5] (3)	Green Colony

Sequence

Name	Concentration
S_ΔTMD1-E0840(1) A	28.9 ng/µL
S_ΔTMD1-E0840(1) B	25.3
S_ΔTMD1-E0840(3) A	26.6
S_ΔTMD1-E0840(3) 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-E0240(1) [pSB4K5] (1)
R0011-E0240(1) [pSB4K5] (2)
R0011-E0240(1) [pSB4K5] (3)
R0011-E0240(1) [pSB4K5] (4)
R0011-E0240(2) [pSB4K5] (1)
R0011-E0240(2) [pSB4K5] (2)
R0011-E0240(2) [pSB4K5] (3)
R0011-E0240(2) [pSB4K5] (4)
I20260 [pSB4K5] (1)
I20260 [pSB4K5] (2)
I20260 [pSB4K5] (3)

Restriction Digestion

Name	Sample	2 buffer	BSA	Enzyme 1		Enzyme 2		MilliQ	Total
R0011-E0240(1) [pSB4K5] (1) [EP]	50 µL	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(1) [pSB4K5] (2) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(1) [pSB4K5] (3) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(1) [pSB4K5] (4) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(2) [pSB4K5] (1) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(2) [pSB4K5] (2) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(2) [pSB4K5] (3) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
R0011-E0240(2) [pSB4K5] (4) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
I20260 [pSB4K5] (1) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
I20260 [pSB4K5] (2) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60
I20260 [pSB4K5] (3) [EP]	50	6	0.6	EcoRI	0.3	PstI	0.3	2.8	60

==Electrophoresis

No.	Name	Length	Results
1	I20260 [pSB4K5] (1) [EP]	960, 4339
2	I20260 [pSB4K5] (2) [EP]	960, 4339
3	I20260 [pSB4K5] (3) [EP]	960, 4339
4	R0011-E0240(1) [pSB4K5] (1) [EP]	980 3378	○
5	R0011-E0240(1) [pSB4K5] (2) [EP]	980 3378	○
6	R0011-E0240(1) [pSB4K5] (3) [EP]	980 3378	}
7	R0011-E0240(1) [pSB4K5] (4) [EP]	980 3378	}
8	R0011-E0240(2) [pSB4K5] (1) [EP]	980 3378	○
9	R0011-E0240(2) [pSB4K5] (2) [EP]	980 3378	}
10	R0011-E0240(2) [pSB4K5] (3) [EP]	980 3378	}
11	R0011-E0240(2) [pSB4K5] (4) [EP]	980 3378	}
12	I20260 [pSB4K5] (1) [EP]	960, 4339	○
13	I20260 [pSB4K5] (2) [EP]	960, 4339	○

White colonies are not inserted R0011 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	MgSO4	dNTPs	10xBuffer	Primer VF2	Primer VR	Template S_Sam7,ΔTMD1-E0840 failed (50ng/µL)	KOD plus ver.2	Total
S_Sam7,ΔTMD1-E0840 (1)	32	3	5	5	1.5	1.5	1	1	50
S_Sam7,ΔTMD1-E0840 (2)	32	3	5	5	1.5	1.5	1	1	50

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

Transformation

Name	Well	Sample	Competent Cell	Total	Plate	Incubation	Colony
S_Sam7,ΔTMD1-E0840 (1)	-	4 µL	50	54	LB (Kan+)	08/06-08/09	○
S_Sam7,ΔTMD1-E0840 (2)	-	4	50	54			○
I20260	2-17-F	2	50	52			○
	2-I-5	2	50	52	LB (Amp+)		○

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

Miniprep

Name	concentration
I20260 [pSB4K5]	116.2 ng/µL
R0011-E0240 [pSB4K5]	146.6

Transfotrmation

Sample	Sample	Competent Cell		Total	Plate	Incuvation	Results
I20260 [pSB4K5]	2 µL	KRX	50	52	LB (Kan+)	08/09 18:00-08/10 12:00	○
R0011-E0240 [pSB4K5]	2	KRX	50	52	LB (Kan+)	08/09 18:00-08/10 12:00	○

Restriction Eigestion and Ethanol Precipitation

To use R0011 for next ligation, we digested it by EcoRI and PstI

Name	Sample	10x Buffer	BSA	Enzyme 1	Enzyme 2	MilliQ	Total	Incubation
R0011 [EP]	50	6	0.6	Enzyme 1	EcoRI	0.5	PstI	0.5	2.4	60	At 37℃ 08/09 16:20-18:20

After restriction enzyme digestion, we did ethanol precipitation.

Ligation and Transformation

Sample	Competent cell		Total	Plate	Incuvation	Colony
R0011 [pSB4K5, KRX]	2 µL	KRX	50	52	LB (Kan+)	08/09 20:00-08/10 09:00	○
R0011 [pSB4K5</partrinfo>, C2]	2	C2	50	52	LB (Kan+)	08/09 20:00-08/10 09:00	○

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

Culture

Cultured I20260 [pSB4K5, R0011-E0240 [pSB4K5], R0011 [pSB4K5, KRX], and R0011 [pSB4K5</partrinfo>, C2].

Minprep

Name	Concentration
S_Sam7,ΔTMD1-E0840 (1-1)	9.9 ng/µL
S_Sam7,ΔTMD1-E0840 (1-2)	27.3
S_Sam7,ΔTMD1-E0840 (2-1)	43.2
S_Sam7,ΔTMD1-E0840 (2-2)	34.7

Culture and Master Plate

At 37℃ 08/09 18:00-08/10 9:00

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

No.	Medium	Cloud	Incubation
1	Kanamycin	○	At 37℃, 08/10 20:00-08/11 9:00
1	Ampicillin	}
2	Kanamycin	○
2	Ampicillin	○
3	Kanamycin	○
3	Ampicillin	}
4	Kanamycin	○
4	Ampicillin	}
5	Kanamycin	○
5	Ampicillin	}
6	Kanamycin	○
6	Ampicillin	○
7	Kanamycin	○
7	Ampicillin	}

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 R0011 [pSB4K5, C2], SRRz 1', 3'

Name	Concentration
R0011 [pSB4K5, C2] (1)	31.2 ng/µL
R0011 [pSB4K5, C2] (3)	29.9

Restriction Digestion and electrophoresis of R0011 [pSB4K5, C2]

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

No.	Name	Length	Results
1	R0011 [pSB4K5, C2] (1-1)
2	R0011 [pSB4K5, C2] (1-2)
3	R0011 [pSB4K5, C2] (1-3)
4	R0011 [pSB4K5, C2] (1-N)
5	R0011 [pSB4K5, C2] (2-1)
6	R0011 [pSB4K5, C2] (2-2)
7	R0011 [pSB4K5, C2] (2-3)
8	R0011 [pSB4K5, C2] (2-N)

Each enzyme correctly cut samples.

Screening PCR of SRRz

No.	Name	Results
1	None
2	Control B0015
3	Control J06702
4	Control B0015
5-24	SRRz-B0015	}

Marker: Lambda Marker Discussion: All of the sample were self-ligation of DT. SRRz weren't inserted.

Thursday, August 12 By: Wataru, Ken

Restriction Digestion and electrophoresis of B0015

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

Maker: Lambda, 100bp Discussion: Each enzyme correctly cut each sample and was active.

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

Miniprep of S_Sam7,ΔTMD1-E0840

Name	Concentration
S_Sam7,ΔTMD1-E0840	29.6 ng/µL

Point mutation PCR of S_Sam7,ΔTMD1-E0840

Name	Template	10xbuffer	dNTPs	MgSO4	Primer Fwd.	Primer Rev.	MilliQ	KOD plus ver.2	Total
S_ΔTMD1-E0840 (1)	1.5	5	5	3	1.5	1.5	31.5	1	50
S_ΔTMD1-E0840 (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℃	10s	30cycles
55℃	30s
68℃	3.5min
4℃	forever

Restriction Digestion by DpnI from 17:50 to 18:50

Electrophoresis

Name
S_ΔTMD1-E0840 (1)
S_ΔTMD1-E0840 (2)
Control

Marker: Lambda, 100bp

Ligation and Transformation

Name	Colony
S_ΔTMD1-E0840 (1)	○
S_ΔTMD1-E0840 (2)	○
Control	}

Friday, August 20 By: Wataru, Ken

Making Culture and Master Plate of S_ΔTMD1-E0840

[[Team:Kyoto/Protocols#Miniprep|Miniprep]

Name	Concentration
B0015	41.1 ng/µL

PCR of SRRz

Name	10xBuffer	MgS04	dNTP	Template	Primer Fwd.		Primer Rev.	MilliQ	KOD plus ver.2	Total
SRRz (1)	5 µL	3	5	5	F1	1.5	1.5	28	1	50
SRRz (2)	5	3	5	5	F2	1.5	1.5	28	1	50
SRRz (3)	5	3	5	5	F1	1.5	1.5	28	1	50
SRRz (4)	5	3	5	5	F2	1.5	1.5	28	1	50
SRRz (5)	5	3	5	5	F1	1.5	1.5	28	1	50
SRRz (6)	5	3	5	5	F2	1.5	1.5	28	1	50

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

Electrophoresis

Name
SRRz (1)
SRRz (3)
SRRz (5)
SRRz (2)
SRRz (4)
SRRz (6)

Discussion: Primer F1 might be better than F2, because the bands of 1, 2 and 3 were clearer. We decided to use sample 1 and 3. Their bands were clearer in the three.

PCR Purification

Name	Concentration
SRRz (1)	134.0 ng/µL
SRRz (3)	69.0

Restriction Digestion

Name	Sample	10xBuffer	100xBuffer	EcoRI	XbaI	SpeI	MilliQ	Total	Incubation
B0015 [EX]	50 µL	6	0.6	0.4	0.4	-	2.6	60	17:45-18:45
SRRz (1) [EP]	50	6	0.6	0.4	-	0.4	2.6	60
SRRz (3) [EP]	50	6	0.6	0.4	-	0.4	2.6	60

Purification

Name	Concentration
SRRz (1) [EP]	109.0 ng/µL
SRRz (2) [EP]	110.0
B0015	25.5

@@ Line 7: / Line 7: @@
 !Name||Well||Sample||Competent Cells||Total||Plate||Incubation||Colony
 |-
-|<partinfo>J23100</partinfo>||1-18-C||1 &micro;L||20||21||rowspan="7"|LB (Amp+)||rowspan="8"|At 37&#x2103;, 7/20 20:50 - 7/21 17:00||&#x25CB;
+|J23100||1-18-C||1 &micro;L||20||21||rowspan="7"|LB (Amp+)||rowspan="8"|At 37&#x2103;, 7/20 20:50 - 7/21 17:00||&#x25CB;
 |-
-|<partinfo>J23105</partinfo>||1-18-M||1||20||21||&#x25CB;
+|J23105||1-18-M||1||20||21||&#x25CB;
 |-
-|<partinfo>J23116</partinfo>||1-20-M||1||20||21||&#x25CB;
+|J23116||1-20-M||1||20||21||&#x25CB;
 |-
-|<partinfo>R0011</partinfo>||1-6-G||1||20||21||&#x25CB;
+|R0011||1-6-G||1||20||21||&#x25CB;
 |-
-|<partinfo>E0840</partinfo>||1-12-O||1||20||21||&#x25CB;
+|E0840||1-12-O||1||20||21||&#x25CB;
 |-
-|<partinfo>J06702</partinfo>||2-8-E||1||20||21||&#x25CB;
+|J06702||2-8-E||1||20||21||&#x25CB;
 |-
-|<partinfo>pSB4K5</partinfo>||1-5-G||1||20||21||&#xD7;
+|pSB4K5||1-5-G||1||20||21||&#xD7;
 |-
-|<partinfo>B0015</partinfo>||1-23-L||1||20||21||LB (Kan+)||&#xD7;
+|B0015||1-23-L||1||20||21||LB (Kan+)||&#xD7;
 |}
-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>.
+A vector of pSB4K5 is Kanamycin-resistance, however, we plated it to LB plate (Amp+). And We didn't pre-culture B0015 despite its vector is Kanamycin-resistance. So, it was predicted that we will fail the transformation of pSB4K5 and B0015.
@@ Line 32: / Line 32: @@
 !Name||Well||Sample||Competent Cells||Total||Plate||Incubation||Colony
 |-
-|<partinfo>pSB4K5</partinfo>||1-5-G||1 &micro;L||20||21||rowspan="2"|LB (Kan+)||rowspan="2"|At 37&#x2103;, 7/21 20:50 - 7/22 16:30||&#x25CB;
+|pSB4K5||1-5-G||1 &micro;L||20||21||rowspan="2"|LB (Kan+)||rowspan="2"|At 37&#x2103;, 7/21 20:50 - 7/22 16:30||&#x25CB;
 |-
-|<partinfo>B0015</partinfo>||1-23-L||1||20||21||&#x25CB;
+|B0015||1-23-L||1||20||21||&#x25CB;
 |}
 =====[[Team:Kyoto/Protocols#Stantard PCR|PCR]] for SRRz and S=====
@@ Line 97: / Line 97: @@
 !Name||Concentration
 |-
-|<partinfo>J23100</partinfo>||18.5 (ng/&micro;L)
+|J23100||18.5 (ng/&micro;L)
 |-
-|<partinfo>J23105</partinfo>||12.5
+|J23105||12.5
 |-
-|<partinfo>J23116</partinfo>||14.6
+|J23116||14.6
 |-
-|<partinfo>R0011</partinfo>||8.6
+|R0011||8.6
 |-
-|<partinfo>E0840</partinfo>||12.1
+|E0840||12.1
 |-
-|<partinfo>J06702</partinfo>||14.7
+|J06702||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>=====
+=====Culture from 07/22 17:00 to 07/23 10:00 and Making Master Plates of pSB4K5 and B0015=====
@@ Line 118: / Line 118: @@
 !Name||Concentration
 |-
-|<partinfo>pSB4K5</partinfo>||79.2 (ng/&micro;L)
+|pSB4K5||79.2 (ng/&micro;L)
 |-
-|<partinfo>B0015</partinfo>||-
+|B0015||-
 |}
-We lost <partinfo>B0015</partinfo> by our mistake. The concentration of <partinfo>pSB4K5</partinfo> is high, so this condition of shaking incubation is moderate.
+We lost B0015 by our mistake. The concentration of pSB4K5 is high, so this condition of shaking incubation is moderate.
 =====[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]=====
 {| class="experiments"
@@ Line 168: / Line 168: @@
 !No.||Name||Sample||10xBuffer||BSA||colspan="2"|Enzyme||MilliQ||Total||Incubation
 |-
-|1||<partinfo>J06702</partinfo>||5 &micro;L||1||0.1||EcoRI||0.1||3.6||10||rowspan="5"|At 37&#x2103; 7/23 18:00 - 7/23 18:30
+|1||J06702||5 &micro;L||1||0.1||EcoRI||0.1||3.6||10||rowspan="5"|At 37&#x2103; 7/23 18:00 - 7/23 18:30
 |-
-|2||<partinfo>J06702</partinfo>||5||1||0.1||XbaI||0.1||3.6||10
+|2||J06702||5||1||0.1||XbaI||0.1||3.6||10
 |-
-|3||<partinfo>J06702</partinfo>||5||1||0.1||SpeI||0.1||3.6||10
+|3||J06702||5||1||0.1||SpeI||0.1||3.6||10
 |-
-|4||<partinfo>J06702</partinfo>||5||1||0.1||PstI||0.1||3.6||10
+|4||J06702||5||1||0.1||PstI||0.1||3.6||10
 |-
-|5||<partinfo>J06702</partinfo>||5||1||0.1||colspan="2"|-||3.7||10
+|5||J06702||5||1||0.1||colspan="2"|-||3.7||10
 |}
 [[Image:KyotoExp100723-1.png|300px|right]]
 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 E0840=====
 {| class="experiments"
 !Name||Sample||10xBuffer||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total||Incubation
@@ Line 189: / Line 189: @@
 |S<sub>Sam7</sub>(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
+|E0840||45||5||EcoRI||0.2||XbaI||0.2||0||50
 |}
 After PCR Purification, evaporated them and diluted 3&micro;L.
@@ Line 195: / Line 195: @@
 !Name||colspan="2"|Vector||colspan="2"|Insert||Ligation High||Total
 |-
-|S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||<partinfo>E0840</partinfo>||0.5&micro;L||S<sub>Sam7</sub>(1)||0.5||1||2
+|S<sub>Sam7</sub>(1)-E0840||E0840||0.5&micro;L||S<sub>Sam7</sub>(1)||0.5||1||2
 |-
-|S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||<partinfo>E0840</partinfo>||0.5||S<sub>Sam7</sub>(2)||0.5||1||2
+|S<sub>Sam7</sub>(2)-E0840||E0840||0.5||S<sub>Sam7</sub>(2)||0.5||1||2
 |}
@@ Line 235: / Line 235: @@
 !Name||Well||Sample||Competent Cell||Total||Plate||Incubation||Colony
 |-
-|<partinfo>E0240</partinfo>||1-12-M||1 &micro;L||20||21||LB (Amp+)||rowspan="3"|At 37&#x2103; 7/26 - 7/27||&#xD7;
+|E0240||1-12-M||1 &micro;L||20||21||LB (Amp+)||rowspan="3"|At 37&#x2103; 7/26 - 7/27||&#xD7;
 |-
-|<partinfo>I20260</partinfo>||2-17-F||1||20||21||rowspan="2"|LB (Kan+)||&#xD7;
+|I20260||2-17-F||1||20||21||rowspan="2"|LB (Kan+)||&#xD7;
 |-
-|<partinfo>J04450</partinfo>||1-5-E||1||20||21||&#xD7;
+|J04450||1-5-E||1||20||21||&#xD7;
 |}
-=====Culture of <partinfo>pSB4K5</partinfo>, <partinfo>E0840</partinfo>, and <partinfo>B0015</partinfo>=====
+=====Culture of pSB4K5, E0840, and B0015=====
 ====Tuesday, July 27 <span class="by">By: Wataru, Tomo, Kazuya, Ken, Naoi====
-=====[[Team:Kyoto/Protocols#Colony PCR|Colony PCR]] of S<sub>Sam7</sub>-<partinfo>E0840</partinfo> (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"
 !No.||Name||Length||Result
 |-
-|1||S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1522||&#x25CB;
+|1||S<sub>Sam7</sub>(1)-E0840||1522||&#x25CB;
 |-
-|2||S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1522||&#xD7;
+|2||S<sub>Sam7</sub>(1)-E0840||1522||&#xD7;
 |-
-|3||S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1522||&#x25CB;
+|3||S<sub>Sam7</sub>(1)-E0840||1522||&#x25CB;
 |-
-|4||S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1522||&#xD7;
+|4||S<sub>Sam7</sub>(1)-E0840||1522||&#xD7;
 |-
-|5||S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1522||&#x25CB;
+|5||S<sub>Sam7</sub>(1)-E0840||1522||&#x25CB;
 |-
-|6||S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1522||&#x25CE; (Use as S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>)
+|6||S<sub>Sam7</sub>(1)-E0840||1522||&#x25CE; (Use as S<sub>Sam7</sub>(1)-E0840)
 |-
-|7||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#xD7;
+|7||S<sub>Sam7</sub>(2)-E0840||1522||&#xD7;
 |-
-|8||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#xD7;
+|8||S<sub>Sam7</sub>(2)-E0840||1522||&#xD7;
 |-
-|9||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#xD7;
+|9||S<sub>Sam7</sub>(2)-E0840||1522||&#xD7;
 |-
-|10||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#xD7;
+|10||S<sub>Sam7</sub>(2)-E0840||1522||&#xD7;
 |-
-|11||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#x25CE; (Use as S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>)
+|11||S<sub>Sam7</sub>(2)-E0840||1522||&#x25CE; (Use as S<sub>Sam7</sub>(2)-E0840)
 |-
-|12||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#x25CB;
+|12||S<sub>Sam7</sub>(2)-E0840||1522||&#x25CB;
 |-
-|13||S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1522||&#x25CB;
+|13||S<sub>Sam7</sub>(2)-E0840||1522||&#x25CB;
 |-
-| +||<partinfo>E0840</partinfo>||1116||
+| +||E0840||1116||
 |-
 | -||None||||
@@ Line 285: / Line 285: @@
 !Name||Concentration
 |-
-|<partinfo>R0011</partinfo>||26.9 ng/&micro;L
+|R0011||26.9 ng/&micro;L
 |-
-|<partinfo>B0015</partinfo>||120.0
+|B0015||120.0
 |-
-|<partinfo>E0840</partinfo>||120.1
+|E0840||120.1
 |}
 =====[[Team:Kyoto/Protocols#RestrictionDigestion|Restriction Digestion]]=====
@@ Line 295: / Line 295: @@
 !Name||Sample||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total||Incubation
 |-
-|<partinfo>B0015</partinfo>||30 &micro;L||5||0.5||EcoRI||0.4||XbaI||0.3||13.7||50||rowspan="3"|At 37&#x2103; 16:45 - 18:00
+|B0015||30 &micro;L||5||0.5||EcoRI||0.4||XbaI||0.3||13.7||50||rowspan="3"|At 37&#x2103; 16:45 - 18:00
 |-
 |SRRz<sub>Sam7</sub>(1)||40||5||0.5||EcoRI||0.4||SpeI||0.4||3.8||50
@@ Line 317: / Line 317: @@
 !Name||Concentration
 |-
-|S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||95.5 ng/&micro;L
+|S<sub>Sam7</sub>(1)-E0840||95.5 ng/&micro;L
 |-
-|S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||98.6
+|S<sub>Sam7</sub>(2)-E0840||98.6
 |}
-Diluted S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo> and S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo> 20 times with water, and used as template DNA.
+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=====
 {| class="experiments"
 !||Water||MgSO4||dNTPs||10xBuffer||Primer Fwd.||Primer Rev.||Template (1)||Template (2)||KOD Plus ver.2||Total
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(1)-<partinfo>E0840</partinfo> (1)||28 &micro;L||3||5||5||1.5||1.5||5||-||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>(1)-E0840 (1)||28 &micro;L||3||5||5||1.5||1.5||5||-||1||50
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(1)-<partinfo>E0840</partinfo> (2)||28||3||5||5||1.5||1.5||5||-||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>(1)-E0840 (2)||28||3||5||5||1.5||1.5||5||-||1||50
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(2)-<partinfo>E0840</partinfo> (1)||28||3||5||5||1.5||1.5||-||5||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>(2)-E0840 (1)||28||3||5||5||1.5||1.5||-||5||1||50
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(2)-<partinfo>E0840</partinfo> (2)||28||3||5||5||1.5||1.5||-||5||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>(2)-E0840 (2)||28||3||5||5||1.5||1.5||-||5||1||50
 |}
 {| class="experiments"
@@ Line 350: / Line 350: @@
 !Name||Sample||fast digestion buffer||DpnI||MilliQ||Total
 |-
-|S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||3 &micro;L||1||0.1||5.8||10
+|S<sub>Sam7</sub>(1)-E0840||3 &micro;L||1||0.1||5.8||10
 |-
-|S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||3||1||0.1||5.8||10
+|S<sub>Sam7</sub>(2)-E0840||3||1||0.1||5.8||10
 |}
 =====[[Team:Kyoto/Protocols#Electrophoresis|Electrophoresis]] for 35min=====
@@ Line 359: / Line 359: @@
 !No.||Name||Length||Result
 |-
-|1||Not digested S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||3363bp||
+|1||Not digested S<sub>Sam7</sub>(1)-E0840||3363bp||
 |-
-|2||Not digested S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||3363||
+|2||Not digested S<sub>Sam7</sub>(2)-E0840||3363||
 |-
-|3||Digested S<sub>Sam7</sub>(1)-<partinfo>E0840</partinfo>||1021, 933, 402, 341, 258, 105, ...||
+|3||Digested S<sub>Sam7</sub>(1)-E0840||1021, 933, 402, 341, 258, 105, ...||
 |-
-|4||Digested S<sub>Sam7</sub>(2)-<partinfo>E0840</partinfo>||1021, 933, 402, 341, 258, 105, ...||
+|4||Digested S<sub>Sam7</sub>(2)-E0840||1021, 933, 402, 341, 258, 105, ...||
 |}
 Marker: 1kb, 100bp
@@ Line 376: / Line 376: @@
 !Name||Sample volume||Fastdigestion Buffer||colspan="2"|Enzyme 1||MilliQ||Total||Incubation
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(1)-<partinfo>E0840</partinfo> (1)||50 &micro;L||6||DpnI||0.2||3.8||60||rowspan="2"|07/29 09:40 - 07/29 11:00
+|S<sub>Sam7,&Delta;TMD1</sub>(1)-E0840 (1)||50 &micro;L||6||DpnI||0.2||3.8||60||rowspan="2"|07/29 09:40 - 07/29 11:00
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(2)-<partinfo>E0840</partinfo> (1)||50||6||DpnI||0.2||3.8||60
+|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]]=====
@@ Line 384: / Line 384: @@
 !Name||Sample||MilliQ||Ligation High||T4 Kinase||Total||Incubation
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(1)-<partinfo>E0840</partinfo> (1)||2 &micro;L||7||5||1||15||rowspan="2"|07/29 11:30 ~ 07/29 13:00
+|S<sub>Sam7,&Delta;TMD1</sub>(1)-E0840 (1)||2 &micro;L||7||5||1||15||rowspan="2"|07/29 11:30 ~ 07/29 13:00
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(2)-<partinfo>E0840</partinfo> (1)||2||7||5||1||15
+|S<sub>Sam7,&Delta;TMD1</sub>(2)-E0840 (1)||2||7||5||1||15
 |}
 =====[[Team:Kyoto/Protocols#Transformation|Transformation]]=====
@@ Line 392: / Line 392: @@
 !Name||Sample Volume||Competent Cell||Total||Plate||Incubation||Colony
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(1)-<partinfo>E0840</partinfo> (1)||3 &micro;L||30||33||rowspan="2"|LB (Amp+)||rowspan="2"|07/29 ~ 07/30||&#x25CB;
+|S<sub>Sam7,&Delta;TMD1</sub>(1)-E0840 (1)||3 &micro;L||30||33||rowspan="2"|LB (Amp+)||rowspan="2"|07/29 ~ 07/30||&#x25CB;
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>(2)-<partinfo>E0840</partinfo> (1)||3||30||33||&#x25CB;
+|S<sub>Sam7,&Delta;TMD1</sub>(2)-E0840 (1)||3||30||33||&#x25CB;
 |}
@@ Line 403: / Line 403: @@
 !Name||Concentration
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||52.7 ng/&micro;L
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1)||52.7 ng/&micro;L
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||54.4
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2)||54.4
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (3)||89.5
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (3)||89.5
 |-
-|<partinfo>pSB4K5</partinfo>||50.7
+|pSB4K5||50.7
 |-
-|<partinfo>R0011</partinfo>||18.6
+|R0011||18.6
 |}
-=====[[Team:Kyoto/Protocols#Standard_PCR|Standard PCR]] of <partinfo>E0240</partinfo>=====
+=====[[Team:Kyoto/Protocols#Standard_PCR|Standard PCR]] of E0240=====
-<partinfo>E0240</partinfo> 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.
+E0240 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"
-!Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template <partinfo>E0240</partinfo>||KOD Pllus ver.2||Total
+!Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template E0240||KOD Pllus ver.2||Total
 |-
-|<partinfo>E0240</partinfo>(1)||28 &micro;L||3||5||5||1.5||1.5||5||1||50
+|E0240(1)||28 &micro;L||3||5||5||1.5||1.5||5||1||50
 |-
-|<partinfo>E0240</partinfo>(2)||28||3||5||5||1.5||1.5||5||1||50
+|E0240(2)||28||3||5||5||1.5||1.5||5||1||50
 |}
 {| class="experiments"
@@ Line 438: / Line 438: @@
 !Name||Concentration
 |-
-|<partinfo>E0240</partinfo>(1)||42.6 ng/&micro;L
+|E0240(1)||42.6 ng/&micro;L
 |-
-|<partinfo>E0240</partinfo>(2)||55.3
+|E0240(2)||55.3
 |}
-=====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] for inserting <partinfo>E0240</partinfo> to <partinfo>pSB4K5</partinfo> by 3A assembly=====
+=====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] for inserting E0240 to pSB4K5 by 3A assembly=====
 {| class="experiments"
 !Name||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
 |-
-|<partinfo>E0240</partinfo>(1) [XP]||30 &micro;L||5||0.5||XbaI||0.2||PstI||0.2||14.1||50
+|E0240(1) [XP]||30 &micro;L||5||0.5||XbaI||0.2||PstI||0.2||14.1||50
 |-
-|<partinfo>E0240</partinfo>(2) [XP]||30||5||0.5||XbaI||0.2||PstI||0.2||14.1||50
+|E0240(2) [XP]||30||5||0.5||XbaI||0.2||PstI||0.2||14.1||50
 |}
 =====PCR Purification=====
@@ Line 454: / Line 454: @@
 !Name||Concentration||Volume
 |-
-|<partinfo>E0240</partinfo>(1) [XP]||21.8 ng/&micro;L||40 &micro;L
+|E0240(1) [XP]||21.8 ng/&micro;L||40 &micro;L
 |-
-|<partinfo>E0240</partinfo>(2) [XP]||32.4||45
+|E0240(2) [XP]||32.4||45
 |}
 Stored at -20&#x2103;.
@@ Line 463: / Line 463: @@
 !Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template (1)||Template (2)||Template (3)||KOD Pllus ver.2||Total
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||32 &micro;L||3||5||5||1.5||1.5||1||-||-||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1)||32 &micro;L||3||5||5||1.5||1.5||1||-||-||1||50
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||32||3||5||5||1.5||1.5||-||1||-||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2)||32||3||5||5||1.5||1.5||-||1||-||1||50
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (3)||32||3||5||5||1.5||1.5||-||-||1||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (3)||32||3||5||5||1.5||1.5||-||-||1||1||50
 |}
 {| class="experiments"
@@ Line 478: / Line 478: @@
 |4&#x2103;||forever||
 |}
-=====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] of S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> by DpnI=====
+=====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]] of S<sub>Sam7,&Delta;TMD1</sub>-E0840 by DpnI=====
 =====[[Team:Kyoto/Protocols#Transformation|Transformation]]=====
 {| class="experiments"
 !Name||Sample||Competent Cells||Total||Plate||Incubation||Colony
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||2 &micro;L||20||22||rowspan="3"|-||rowspan="3"|-||&#x25CB;
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1)||2 &micro;L||20||22||rowspan="3"|-||rowspan="3"|-||&#x25CB;
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||2||20||22||&#x7D;
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2)||2||20||22||&#x7D;
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (3)||2||20||22||&#x25CB;
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (3)||2||20||22||&#x25CB;
 |}
 ====Tuesday, August 3 <span class="by">By: </span>====
 =====Culture=====
-Picked two colonies from S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1), and S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (3), and cultured at 37&#x2103; from 08/03 to 08/04.
+Picked two colonies from S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1), and S<sub>Sam7,&Delta;TMD1</sub>-E0840 (3), and cultured at 37&#x2103; from 08/03 to 08/04.
 =====[[Team:Kyoto/Protocols#Miniprep|Miniprep]]=====
 {| class="experiments"
 !Name||Concentration
 |-
-|<partinfo>pSB4K5</partinfo>||60.7 ng/&micro;L
+|pSB4K5||60.7 ng/&micro;L
 |-
-|<partinfo>R0011</partinfo>||26.8
+|R0011||26.8
 |}
 =====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]]=====
@@ Line 505: / Line 505: @@
 !Name||Sample||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
 |-
-|<partinfo>R0011</partinfo> [ES]||50 &micro;L||6||0.6||EcoRI||0.2||SpeI||0.2||3||60
+|R0011 [ES]||50 &micro;L||6||0.6||EcoRI||0.2||SpeI||0.2||3||60
 |-
-|<partinfo>pSB4K5</partinfo> [EP]||50||6||0.6||EcoRI||0.2||PstI||0.2||3||60
+|pSB4K5 [EP]||50||6||0.6||EcoRI||0.2||PstI||0.2||3||60
 |-
-|<partinfo>E0240</partinfo>(1) [XP]||50||6||0.6||XbaI||0.2||PstI||0.2||3||60
+|E0240(1) [XP]||50||6||0.6||XbaI||0.2||PstI||0.2||3||60
 |-
-|<partinfo>E0240</partinfo>(2) [XP]||50||6||0.6||XbaI||0.2||PstI||0.2||3||60
+|E0240(2) [XP]||50||6||0.6||XbaI||0.2||PstI||0.2||3||60
 |}
 =====PCR Purification=====
@@ Line 517: / Line 517: @@
 !Name||Concentration
 |-
-|<partinfo>pSB4K5</partinfo> [EP]||39.5 ng/&micro;L
+|pSB4K5 [EP]||39.5 ng/&micro;L
 |-
-|<partinfo>E0240</partinfo>(1) [XP]||21.8
+|E0240(1) [XP]||21.8
 |-
-|<partinfo>E0240</partinfo>(2) [XP]||32.4
+|E0240(2) [XP]||32.4
 |}
-<partinfo>pSB4K5</partinfo> [EP] is concentrated 10&micro;L and <partinfo>E0240</partinfo>(1) [XP], <partinfo>E0240</partinfo>(2) [XP] are concentrated 1&micro;L.
+pSB4K5 [EP] is concentrated 10&micro;L and E0240(1) [XP], E0240(2) [XP] are concentrated 1&micro;L.
 =====Ethanol Precipitation=====
-After ethanol precipitation, we diluted <partinfo>pSB4K5</partinfo> by 2&micro;L MilliQ
+After ethanol precipitation, we diluted pSB4K5 by 2&micro;L MilliQ
 =====[[Team:Kyoto/Protocols#Ligation|Ligation]]=====
 {| class="experiments"
 !Name||Vector||colspan="2"|Insert 1||colspan="2"|Insert 2||Ligation High||Total||Incubation
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>]||<partinfo>pSB4K5</partinfo> [EP]||1||<partinfo>R0011</partinfo>  [ES]||1||<partinfo>E0240</partinfo>(1) [XP]||1||3||15||rowspan="2"|17:30 - 20:20
+|R0011-E0240(1) [pSB4K5]||pSB4K5 [EP]||1||R0011  [ES]||1||E0240(1) [XP]||1||3||15||rowspan="2"|17:30 - 20:20
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>]||<partinfo>pSB4K5</partinfo> [EP]||1||<partinfo>R0011</partinfo> [ES]||1||<partinfo>E0240</partinfo>(2) [XP]||1||3||15
+|R0011-E0240(2) [pSB4K5]||pSB4K5 [EP]||1||R0011 [ES]||1||E0240(2) [XP]||1||3||15
 |}
-=====[[Team:Kyoto/Protocols#Standard PCR|Standard PCR]] of <partinfo>I20260</partinfo>=====
+=====[[Team:Kyoto/Protocols#Standard PCR|Standard PCR]] of I20260=====
 {| class="experiments"
-!Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template <partinfo>I20260</partinfo>||KOD plus ver.2||Total
+!Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template I20260||KOD plus ver.2||Total
 |-
-|<partinfo>I20260</partinfo> (1)||32&micro;L||3||5||5||1.5||1.5||1||1||50
+|I20260 (1)||32&micro;L||3||5||5||1.5||1.5||1||1||50
 |-
-|<partinfo>I20260</partinfo> (2)||32||3||5||5||1.5||1.5||-||1||50
+|I20260 (2)||32||3||5||5||1.5||1.5||-||1||50
 |}
 {| class="experiments"
@@ Line 557: / Line 557: @@
 !Name||Concentration
 |-
-|<partinfo>I20260</partinfo>||40.6 ng/&micro;L
+|I20260||40.6 ng/&micro;L
 |}
 =====[[Team:Kyoto/Protocols#Restriction Digestion|Restriction Digestion]]=====
@@ Line 563: / Line 563: @@
 !Name||Sample volume||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
 |-
-|<partinfo>I20260</partinfo> [EP]||45 &micro;L||6||0.6||EcoRI||0.2||PstI||0.2||8||60
+|I20260 [EP]||45 &micro;L||6||0.6||EcoRI||0.2||PstI||0.2||8||60
 |}
 =====[[Team:Kyoto/Protocols#PCR Purification|PCR Purification]]=====
@@ Line 569: / Line 569: @@
 !Name||Concentration||Volume
 |-
-|<partinfo>I20260</partinfo> [EP]||74.1 ng/&micro;L||30
+|I20260 [EP]||74.1 ng/&micro;L||30
 |}
-<partinfo>I20260</partinfo> [EP] is concentrated at 7&micro;L
+I20260 [EP] is concentrated at 7&micro;L
 =====[[Team:Kyoto/Protocols#Ligation|Ligation]]=====
 {| class="experiments"
 !||Vector||colspan="2"|Insert||colspan="2"|Ligation High||Total||Incubation
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>]||<partinfo>pSB4K5</partinfo> [EP]||1||<partinfo>I20260</partinfo> [EP]||1||2||4||20:00-20:30
+|I20260 [pSB4K5]||pSB4K5 [EP]||1||I20260 [EP]||1||2||4||20:00-20:30
 |}
 <div class="measure-construction">
@@ Line 583: / Line 583: @@
 !Name||Sample||Competent Cell||Total||Plate||Incubation||Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>]||1 &micro;L||20||21||rowspan="3"|LB (Kan+)||rowspan="3"|08/03-08/04||&#x25CB;
+|R0011-E0240(1) [pSB4K5]||1 &micro;L||20||21||rowspan="3"|LB (Kan+)||rowspan="3"|08/03-08/04||&#x25CB;
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>]||1||20||21||&#x25CB;
+|R0011-E0240(2) [pSB4K5]||1||20||21||&#x25CB;
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>]||1||20||21||&#x25CB;
+|I20260 [pSB4K5]||1||20||21||&#x25CB;
 |}
@@ Line 593: / Line 593: @@
 ====Thursday, August 5 <span class="by">By: </span>====
 =====Culture and Master Plates=====
-<partinfo>pSB4K5</partinfo> 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.
+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 <partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] and <partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] plate. We cultured both white and green colonies.
+However, white colonies and green colonies are observed in R0011-E0240(1) [pSB4K5] and R0011-E0240(2) [pSB4K5] plate. We cultured both white and green colonies.
-In <partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>], Many of colonies are red, but green colonies are observed. We cultured green colonies.
+In I20260 [pSB4K5], Many of colonies are red, but green colonies are observed. We cultured green colonies.
 {| class="experiments"
 !Name||Color||Incubation
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (1)||Green Colony||rowspan="11"|8/5-8/6
+|R0011-E0240(1) [pSB4K5] (1)||Green Colony||rowspan="11"|8/5-8/6
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (2)||Green Colony
+|R0011-E0240(1) [pSB4K5] (2)||Green Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (3)||White Colony
+|R0011-E0240(1) [pSB4K5] (3)||White Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (4)||White Colony
+|R0011-E0240(1) [pSB4K5] (4)||White Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (1)||Green Colony
+|R0011-E0240(2) [pSB4K5] (1)||Green Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (2)||White Colony
+|R0011-E0240(2) [pSB4K5] (2)||White Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (3)||White Colony
+|R0011-E0240(2) [pSB4K5] (3)||White Colony
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (4)||White Colony
+|R0011-E0240(2) [pSB4K5] (4)||White Colony
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (1)||Green Colony
+|I20260 [pSB4K5] (1)||Green Colony
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (2)||Green Colony
+|I20260 [pSB4K5] (2)||Green Colony
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (3)||Green Colony
+|I20260 [pSB4K5] (3)||Green Colony
 |}
 =====Sequence=====
@@ Line 627: / Line 627: @@
 !Name||Concentration
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo>(1) A||28.9 ng/&micro;L
+|S<sub>&Delta;TMD1</sub>-E0840(1) A||28.9 ng/&micro;L
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo>(1) B||25.3
+|S<sub>&Delta;TMD1</sub>-E0840(1) B||25.3
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo>(3) A||26.6
+|S<sub>&Delta;TMD1</sub>-E0840(3) A||26.6
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo>(3) B||24.0
+|S<sub>&Delta;TMD1</sub>-E0840(3) 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.
@@ Line 643: / Line 643: @@
 !Name
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (1)
+|R0011-E0240(1) [pSB4K5] (1)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (2)
+|R0011-E0240(1) [pSB4K5] (2)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (3)
+|R0011-E0240(1) [pSB4K5] (3)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (4)
+|R0011-E0240(1) [pSB4K5] (4)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (1)
+|R0011-E0240(2) [pSB4K5] (1)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (2)
+|R0011-E0240(2) [pSB4K5] (2)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (3)
+|R0011-E0240(2) [pSB4K5] (3)
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (4)
+|R0011-E0240(2) [pSB4K5] (4)
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (1)
+|I20260 [pSB4K5] (1)
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (2)
+|I20260 [pSB4K5] (2)
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (3)
+|I20260 [pSB4K5] (3)
 |}
 =====Restriction Digestion=====
@@ Line 669: / Line 669: @@
 !Name||Sample||2 buffer||BSA||colspan="2"|Enzyme 1||colspan="2"|Enzyme 2||MilliQ||Total
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (1) [EP]||50 &micro;L||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(1) [pSB4K5] (1) [EP]||50 &micro;L||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (2) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(1) [pSB4K5] (2) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (3) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(1) [pSB4K5] (3) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (4) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(1) [pSB4K5] (4) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (1) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(2) [pSB4K5] (1) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (2) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(2) [pSB4K5] (2) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (3) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(2) [pSB4K5] (3) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (4) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|R0011-E0240(2) [pSB4K5] (4) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (1) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|I20260 [pSB4K5] (1) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (2) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|I20260 [pSB4K5] (2) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (3) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
+|I20260 [pSB4K5] (3) [EP]||50||6||0.6||EcoRI||0.3||PstI||0.3||2.8||60
 |}
 ========Electrophoresis======
@@ Line 695: / Line 695: @@
 !No.||Name||Length||Results
 |-
-|1||<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (1) [EP]||960, 4339||
+|1||I20260 [pSB4K5] (1) [EP]||960, 4339||
 |-
-|2||<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (2) [EP]||960, 4339||
+|2||I20260 [pSB4K5] (2) [EP]||960, 4339||
 |-
-|3||<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (3) [EP]||960, 4339||
+|3||I20260 [pSB4K5] (3) [EP]||960, 4339||
 |-
-|4||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (1) [EP]||980 3378||&#x25CB;
+|4||R0011-E0240(1) [pSB4K5] (1) [EP]||980 3378||&#x25CB;
 |-
-|5||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (2) [EP]||980 3378||&#x25CB;
+|5||R0011-E0240(1) [pSB4K5] (2) [EP]||980 3378||&#x25CB;
 |-
-|6||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (3) [EP]||980 3378||&#x7D;
+|6||R0011-E0240(1) [pSB4K5] (3) [EP]||980 3378||&#x7D;
 |-
-|7||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(1) [<partinfo>pSB4K5</partinfo>] (4) [EP]||980 3378||&#x7D;
+|7||R0011-E0240(1) [pSB4K5] (4) [EP]||980 3378||&#x7D;
 |-
-|8||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (1) [EP]||980 3378||&#x25CB;
+|8||R0011-E0240(2) [pSB4K5] (1) [EP]||980 3378||&#x25CB;
 |-
-|9||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (2) [EP]||980 3378||&#x7D;
+|9||R0011-E0240(2) [pSB4K5] (2) [EP]||980 3378||&#x7D;
 |-
-|10||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (3) [EP]||980 3378||&#x7D;
+|10||R0011-E0240(2) [pSB4K5] (3) [EP]||980 3378||&#x7D;
 |-
-|11||<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo>(2) [<partinfo>pSB4K5</partinfo>] (4) [EP]||980 3378||&#x7D;
+|11||R0011-E0240(2) [pSB4K5] (4) [EP]||980 3378||&#x7D;
 |-
-|12||<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (1) [EP]||960, 4339||&#x25CB;
+|12||I20260 [pSB4K5] (1) [EP]||960, 4339||&#x25CB;
 |-
-|13||<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>] (2) [EP]||960, 4339||&#x25CB;
+|13||I20260 [pSB4K5] (2) [EP]||960, 4339||&#x25CB;
 |}
 [[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 ''lac''I gene.
+White colonies are not inserted R0011 but its vector. Top10 we used are deleted Lac operon. Then, correctly inserted parts is green because of the lack of ''lac''I gene.
 =====Error PCR (Retry)=====
 {| class="experiments"
-!Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> failed (50ng/&micro;L)||KOD plus ver.2||Total
+!Name||Water||MgSO4||dNTPs||10xBuffer||Primer VF2||Primer VR||Template S<sub>Sam7,&Delta;TMD1</sub>-E0840 failed (50ng/&micro;L)||KOD plus ver.2||Total
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||32||3||5||5||1.5||1.5||1||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1)||32||3||5||5||1.5||1.5||1||1||50
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||32||3||5||5||1.5||1.5||1||1||50
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2)||32||3||5||5||1.5||1.5||1||1||50
 |}
 {| class="experiments"
@@ Line 748: / Line 748: @@
 !Name||Well||Sample||Competent Cell||Total||Plate||Incubation||Colony
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||-||4 &micro;L||50||54||rowspan="3"|LB (Kan+)||rowspan="4"|08/06-08/09||&#x25CB;
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1)||-||4 &micro;L||50||54||rowspan="3"|LB (Kan+)||rowspan="4"|08/06-08/09||&#x25CB;
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||-||4||50||54||&#x25CB;
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2)||-||4||50||54||&#x25CB;
 |-
-|<partinfo>I20260</partinfo>||2-17-F||2||50||52||&#x25CB;
+|I20260||2-17-F||2||50||52||&#x25CB;
 |-
 |||2-I-5||2||50||52||LB (Amp+)||&#x25CB;
@@ Line 763: / Line 763: @@
 !Name||concentration
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>]||116.2 ng/&micro;L
+|I20260 [pSB4K5]||116.2 ng/&micro;L
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo> [<partinfo>pSB4K5</partinfo>]||146.6
+|R0011-E0240 [pSB4K5]||146.6
 |}
 =====Transfotrmation=====
@@ Line 771: / Line 771: @@
 !Sample||Sample||colspan="2"|Competent Cell||Total||Plate||Incuvation||Results
 |-
-|<partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>]||2 &micro;L||KRX||50||52||rowspan="2"|LB (Kan+)||rowspan="2"|08/09 18:00-08/10 12:00||&#x25CB;
+|I20260 [pSB4K5]||2 &micro;L||KRX||50||52||rowspan="2"|LB (Kan+)||rowspan="2"|08/09 18:00-08/10 12:00||&#x25CB;
 |-
-|<partinfo>R0011</partinfo>-<partinfo>E0240</partinfo> [<partinfo>pSB4K5</partinfo>]||2||KRX||50||52||&#x25CB;
+|R0011-E0240 [pSB4K5]||2||KRX||50||52||&#x25CB;
 |}
 =====Restriction Eigestion and Ethanol Precipitation=====
-To use <partinfo>R0011</partinfo> for next ligation, we digested it by EcoRI and PstI
+To use R0011 for next ligation, we digested it by EcoRI and PstI
 {| class="experiments"
 !Name||Sample||10x Buffer||BSA||rowspan="2"|Enzyme 1||Enzyme 2||MilliQ||Total||Incubation
 |-
-|<partinfo>R0011</partinfo> [EP]||50||6||0.6||EcoRI||0.5||PstI||0.5||2.4||60||At 37&#x2103; 08/09 16:20-18:20
+|R0011 [EP]||50||6||0.6||EcoRI||0.5||PstI||0.5||2.4||60||At 37&#x2103; 08/09 16:20-18:20
 |}
 After restriction enzyme digestion, we did ethanol precipitation.
@@ Line 787: / Line 787: @@
 !Name|Sample||colspan="2"|Competent cell||Total||Plate||Incuvation||Colony
 |-
-|<partinfo>R0011</partinfo> [<partinfo>pSB4K5</partinfo>, KRX]||2 &micro;L||KRX||50||52||rowspan="2"|LB (Kan+)||rowspan="2"|08/09 20:00-08/10 09:00||&#x25CB;
+|R0011 [pSB4K5, KRX]||2 &micro;L||KRX||50||52||rowspan="2"|LB (Kan+)||rowspan="2"|08/09 20:00-08/10 09:00||&#x25CB;
 |-
-|<partinfo>R0011</partinfo> [<partinfo>pSB4K5</partrinfo>, C2]||2||C2||50||52||&#x25CB;
+|R0011 [pSB4K5</partrinfo>, C2]||2||C2||50||52||&#x25CB;
 |}
@@ Line 795: / Line 795: @@
 ====Tuesday, August 10 <span class="by">By: Wataru, Tomonori, Ken, Fumitaka</span>
 =====Culture=====
-Cultured <partinfo>I20260</partinfo> [<partinfo>pSB4K5</partinfo>, <partinfo>R0011</partinfo>-<partinfo>E0240</partinfo> [<partinfo>pSB4K5</partinfo>], <partinfo>R0011</partinfo> [<partinfo>pSB4K5</partinfo>, KRX], and <partinfo>R0011</partinfo> [<partinfo>pSB4K5</partrinfo>, C2].
+Cultured I20260 [pSB4K5, R0011-E0240 [pSB4K5], R0011 [pSB4K5, KRX], and R0011 [pSB4K5</partrinfo>, C2].
 =====Minprep=====
 {| class="experiments"
 !Name||Concentration
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1-1)||9.9 ng/&micro;L
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1-1)||9.9 ng/&micro;L
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1-2)||27.3
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (1-2)||27.3
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2-1)||43.2
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2-1)||43.2
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2-2)||34.7
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840 (2-2)||34.7
 |}
 =====Culture and Master Plate=====
@@ Line 845: / Line 845: @@
 |}
 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 <partinfo>R0011</partinfo> [pSB4K5, C2], SRRz 1', 3'=====
+=====Miniprep of R0011 [pSB4K5, C2], SRRz 1', 3'=====
 {| class="experiments"
 !Name||Concentration
 |-
-|<partinfo>R0011</partinfo> [pSB4K5, C2] (1)||31.2 ng/&micro;L
+|R0011 [pSB4K5, C2] (1)||31.2 ng/&micro;L
 |-
-|<partinfo>R0011</partinfo> [pSB4K5, C2] (3)||29.9
+|R0011 [pSB4K5, C2] (3)||29.9
 |}
-=====Restriction Digestion and electrophoresis of <partinfo>R0011</partinfo> [pSB4K5, C2]=====
+=====Restriction Digestion and electrophoresis of R0011 [pSB4K5, C2]=====
 {| class="experiments"
 !Name||EcoRI||PstI
@@ Line 869: / Line 869: @@
 !No.||Name||Length||Results
 |-
-|1||<partinfo>R0011</partinfo> [pSB4K5, C2] (1-1)||||
+|1||R0011 [pSB4K5, C2] (1-1)||||
 |-
-|2||<partinfo>R0011</partinfo> [pSB4K5, C2] (1-2)||||
+|2||R0011 [pSB4K5, C2] (1-2)||||
 |-
-|3||<partinfo>R0011</partinfo> [pSB4K5, C2] (1-3)||||
+|3||R0011 [pSB4K5, C2] (1-3)||||
 |-
-|4||<partinfo>R0011</partinfo> [pSB4K5, C2] (1-N)||||
+|4||R0011 [pSB4K5, C2] (1-N)||||
 |-
-|5||<partinfo>R0011</partinfo> [pSB4K5, C2] (2-1)||||
+|5||R0011 [pSB4K5, C2] (2-1)||||
 |-
-|6||<partinfo>R0011</partinfo> [pSB4K5, C2] (2-2)||||
+|6||R0011 [pSB4K5, C2] (2-2)||||
 |-
-|7||<partinfo>R0011</partinfo> [pSB4K5, C2] (2-3)||||
+|7||R0011 [pSB4K5, C2] (2-3)||||
 |-
-|8||<partinfo>R0011</partinfo> [pSB4K5, C2] (2-N)||||
+|8||R0011 [pSB4K5, C2] (2-N)||||
 |}
 [[image:KyotoExp100811-1.png]]
@@ Line 893: / Line 893: @@
 |1||None||
 |-
-|2||Control <partinfo>B0015</partinfo>||
+|2||Control B0015||
 |-
-|3||Control <partinfo>J06702</partinfo>||
+|3||Control J06702||
 |-
-|4||Control <partinfo>B0015</partinfo>||
+|4||Control B0015||
 |-
-|5-24||SRRz-<partinfo>B0015</partinfo>||&#x7D;
+|5-24||SRRz-B0015||&#x7D;
 |}
 Marker: Lambda Marker
@@ Line 908: / Line 908: @@
 ====Thursday, August 12 <span class="by">By: Wataru, Ken</span>====
-=====Restriction Digestion and electrophoresis of <partinfo>B0015</partinfo>=====
+=====Restriction Digestion and electrophoresis of B0015=====
 {| class="experiments"
 !Name||Template||10xbuffer||100xbuffer||EcoRI||XbaI 1||XbaI 2||SpeI||PstI 1||PstI 2||Water||Total
@@ Line 932: / Line 932: @@
 ====Thursday, August 19 <span class="by">By: Wataru, Tomo, Ken</span>
-=====Miniprep of S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo>=====
+=====Miniprep of S<sub>Sam7,&Delta;TMD1</sub>-E0840=====
 {| class="experiments"
 !Name||Concentration
 |-
-|S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo>||29.6 ng/&micro;L
+|S<sub>Sam7,&Delta;TMD1</sub>-E0840||29.6 ng/&micro;L
 |}
-=====Point mutation PCR of S<sub>Sam7,&Delta;TMD1</sub>-<partinfo>E0840</partinfo>=====
+=====Point mutation PCR of S<sub>Sam7,&Delta;TMD1</sub>-E0840=====
 {| class="experiments"
 !Name||Template||10xbuffer||dNTPs||MgSO4||Primer Fwd.||Primer Rev.||MilliQ||KOD plus ver.2||Total
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||1.5||5||5||3||1.5||1.5||31.5||1||50
+|S<sub>&Delta;TMD1</sub>-E0840 (1)||1.5||5||5||3||1.5||1.5||31.5||1||50
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||1.5||5||5||3||1.5||1.5||31.5||1||50
+|S<sub>&Delta;TMD1</sub>-E0840 (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
@@ Line 964: / Line 964: @@
 !Name
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)
+|S<sub>&Delta;TMD1</sub>-E0840 (1)
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)
+|S<sub>&Delta;TMD1</sub>-E0840 (2)
 |-
 |Control
@@ Line 976: / Line 976: @@
 !Name||Colony
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (1)||&#x25CB;
+|S<sub>&Delta;TMD1</sub>-E0840 (1)||&#x25CB;
 |-
-|S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo> (2)||&#x25CB;
+|S<sub>&Delta;TMD1</sub>-E0840 (2)||&#x25CB;
 |-
 |Control||&#x7D;
@@ Line 985: / Line 985: @@
 ====Friday, August 20 <span class="by">By: Wataru, Ken</span>====
-=====Making Culture and Master Plate of S<sub>&Delta;TMD1</sub>-<partinfo>E0840</partinfo>=====
+=====Making Culture and Master Plate of S<sub>&Delta;TMD1</sub>-E0840=====
 =====[[Team:Kyoto/Protocols#Miniprep|Miniprep]=====
 {| class="expeirments"
 !Name||Concentration
 |-
-|<partinfo>B0015</partinfo>||41.1 ng/&micro;L
+|B0015||41.1 ng/&micro;L
 |}
 =====[[Team:Kyoto/Protocols#Standard PCR|PCR]] of SRRz=====
@@ Line 1,049: / Line 1,049: @@
 !Name||Sample||10xBuffer||100xBuffer||EcoRI||XbaI||SpeI||MilliQ||Total||Incubation
 |-
-|<partinfo>B0015</partinfo> [EX]||50 &micro;L||6||0.6||0.4||0.4||-||2.6||60||rowspan="3"|17:45-18:45
+|B0015 [EX]||50 &micro;L||6||0.6||0.4||0.4||-||2.6||60||rowspan="3"|17:45-18:45
 |-
 |SRRz (1) [EP]||50||6||0.6||0.4||-||0.4||2.6||60
@@ Line 1,063: / Line 1,063: @@
 |SRRz (2) [EP]||110.0
 |-
-|<partinfo>B0015</partinfo>||25.5
+|B0015||25.5
 |}
 =====[[Team:Kyoto/Protocols#Ligation|Ligation]] and [[Team:Kyoto/Protocols#Transformation]]=====
 ----

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

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/Notebook1

From 2010.igem.org

Revision as of 12:13, 23 October 2010

Contents

Notebook

Construction for Lysisbox

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

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

PCR for SRRz and S

Thursday, July 22 By: Wataru

Electrophoresis (40min) of the PCR Products

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

Friday, July 23 By: Wataru, Tomo, Makoto

PCR for SRRz

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

Restriction Digestion and Ligation to insert S gene to E0840

Monday, July 26 By: Wataru, Tomonori, Makoto

Electrophoresis of PCR Products

PCR Purification

Culture of pSB4K5, E0840, and B0015

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

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

Wednesday, July 28 By:

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:

Ligation and Phosphorylation

Monday, August 2 By: Wataru, Ken

Standard PCR of E0240

Restriction Digestion for inserting E0240 to pSB4K5 by 3A assembly

PCR Purification

Error PCR

Restriction Digestion of SSam7,ΔTMD1-E0840 by DpnI

Tuesday, August 3 By:

Culture

PCR Purification

Ethanol Precipitation

Standard PCR of I20260

Transformation

Thursday, August 5 By:

Culture and Master Plates

Sequence

Friday, August 6

Miniprep

Restriction Digestion

==Electrophoresis

Error PCR (Retry)

Transformation

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

Miniprep

Transfotrmation

Restriction Eigestion and Ethanol Precipitation

Ligation and Transformation

Culture

Minprep

Culture and Master Plate

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

Miniprep of R0011 [pSB4K5, C2], SRRz 1', 3'

Restriction Digestion and electrophoresis of R0011 [pSB4K5, C2]

Screening PCR of SRRz

Thursday, August 12 By: Wataru, Ken

Restriction Digestion and electrophoresis of B0015

Miniprep of SSam7,ΔTMD1-E0840

Point mutation PCR of SSam7,ΔTMD1-E0840

Restriction Digestion by DpnI from 17:50 to 18:50

Electrophoresis

Ligation and Transformation

Friday, August 20 By: Wataru, Ken

Making Culture and Master Plate of SΔTMD1-E0840

[[Team:Kyoto/Protocols#Miniprep|Miniprep]

PCR of SRRz

Purification

Ligation and Team:Kyoto/Protocols#Transformation

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

Restriction Digestion of S_Sam7,ΔTMD1-E0840 by DpnI

Miniprep of S_Sam7,ΔTMD1-E0840

Point mutation PCR of S_Sam7,ΔTMD1-E0840

Making Culture and Master Plate of S_ΔTMD1-E0840

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