Team:Paris Bettencourt/SebaTemplate

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Revision as of 05:23, 27 October 2013

Detect

Saturday 13th August

PCR circular and linear, Conjugation of XL-10 (with sSP011), Patches, Digestion M13 backbone, RFP insert, Gel of PCR

PCR circular and linear, 40.5°C, 60° of pSB1A3, pSB1C3

ReagentVolume
1x
Nuclease-free water37.25 ul
5x Phusion HF Buffer10 ul
10 mM dNTPs1 ul
Forward Primer (10 uM)0.5 ul
Reverse Primer (10 uM)0.5 ul
Template Plasmid0.25 ul
Phusion DNA Polymerase0.5 ul
Total Volume50 ul


Thermocycler Protocol: NEB Phusion
TempTime
Start98°C30 secMelt
Cycle 198°C5 secMelt 35 cycles
Cycle 240.5°C / 60°C 25 secAnneal
Cycle 372°C5 minExtend
Finish72°C5 minExtend
Store10°CForeverStore


Conjugation of XL-10 (with sSP011)
1) From O/N cultures Dilute strains 1/100 in LB
2) Wait for OD to reach O,2
3) Prepare tube (in BD tubes) :
- Tube = 0,5mL LB with Strain (sSP011) + 0,5mL LB with Strain (XL-10 Kan)
4) Incubate 2 hours at 37°C (actually not in the shaker, but we accidently kept them in the shaker...)
5) Plate 20ul for mixed tube on LB antiobiotics (Tet, Kan)
6) Incubate overnight at 37°C


Patches
check and make new ones


Digestion M13 backbone, RFP insert
for Backbone (M13mp18 plasmid): 3ug
7,58 ul plasmid (c=395ng/ul)
3 ul EcoRI
3 ul PstI
3ul 10x Fast Digest
13,42 ul H20
incubate for 12 min on 37°
heat inactivation: 80° 5 min
for insert (BBa_J04450): 5ug
31,4 ul plasmid
5 ul EcoRi
5 ul PstI
3,6 ul H20
incubate for 20 min at 37°
heat inactivation: 80° 5min

Gel of PCR (Amp 40.5 circ, lin, Chl 60° lin, circ)
100V, 20 min 1% gel

Detect

Sunday 14th July

Gel of PCR, Gel Extraction, DpnI digest of PCR products and PCR purification

Gel of PCR (Amp 60° circ, lin, Chl 40.5 circ, lin)
100V, 20 min 1% gel

Gel of Digest
100V, 20 min 1% gel

Gel Extraction
Excise the DNA fragment from the agarose gel with a clean, sharp scalpel. Minimize the size of the gel slice by removing extra agarose.
Weigh the gel slice in a colorless tube. Add 3 volumes of Buffer QG to 1 volume of gel (100 mg ~ 100 μl). To help dissolve gel, mix by vortexing the tube every 2–3 min during the incubation. After the gel slice has dissolved completely, check that the color of the mixture is yellow (similar to Buffer QG without dissolved agarose).
Add 1 gel volume of isopropanol to the sample and mix (actually only needed for very small products or very big products)
To bind DNA, apply the sample to the QIAquick column, and centrifuge for 1 min.
Discard flow-through and place QIAquick column back in the same collection tube.
To wash, add 0.75 ml of Buffer PE to QIAquick column and centrifuge for 1 min.
11. Discard the flow-through and centrifuge the QIAquick column for an additional 1 min at 17,900 x g (13,000 rpm). 12. Place QIAquick column into a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl elution buffer to the center of the QIAquick membrane, let the column stand for 1 min, and then centrifuge for 1 min.


DpnI digest of PCR products:
SPCR4 (40ul) - add 1 ul DpnI
SPCR 7 (150ul) - add 3 ul of DpnI
SPCR8 (60 ul) - add 3 ul of DpnI
SPCR 9 (150ul) - add 3 ul of DpnI
SPCR10 (110ul) - add 3 ul of DpnI
Incubate for 15 min at 37°C


PCR purification
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 50 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Detect

Monday 15th July

Plating and control of antibiotic resistance.

We made a 1:1000 dilution of KAN (stand.c) in an LB solid media.

Pouring the plates. Around 20 mL/plate
1. KEIOΔPYR KANR Growth
2. ME1655 KANR No growth

Conclusion :

The KEIOΔPYRF growed as expected. Negative control did not growth.
Plates have KAN antibiotic
KEIO has KAN R.

Detect

Tuesday 16th July

We prepared a colony PCR to send the KAN for sequencing, to know exactly the sequence of the KAN.

KEIOΔMPYRF has a deletion of PYRF to be replaced by KAN
We pitched 4 singles colonies into 50µL of H2O
Boil 5 minutes at 95°C
1,5 µL of this can be used directly for PCR

PCR reaction
Keep all the regents at 4°C while preparing the mixture

ReagentVolume
JW 182 (10 uM)
JW 183 (10 uM)
Template DNA
Quick-load Tag 2x Master Mix
Nuclease free water		0,5 µL
0,5 µL
1,5 µL
12,5 µL
10 µL
Total volume25 µL


Thermocycler Protocol : NEB Quick-Load

Temperature Time
Start

Cycle1
Cycle 2
Cycle 3

Finish
Store		 95°C

95°C
50°C
68°C

68°C
10°C		 30 seconds

15 seconds
30 seconds
1 minute/kB

5 minutes
Forever		 melt

melt
anneal
extend - 35 cycles

extend
store

Gel electrophoresis

We do it to prove that our colony PCR was successful. We expect a band at about 800 base pairs.
Our gel is 1%, therefore we used 0,5g agarose in 100µL TAE buffer.
As a ladder, we used a 1kB plus gene ruler of fermentor.
We l the gel with 5 µL sample ans we kept the sample at 4°C.

PICTURE

We see that the band are as expected. THis is an indicator that KAN is at the right place. The sequence has then been sent for sequencing

Transformation of PAUC 18 into a NEBΔturbo clearing cells
We are transforming PAUC 18 that consist in a low ORI and ampicillin resistance
We will use commercialized NEB turbo competent cells as well as freshly made chemical competent cells
We did this to check the competency of our fresh competent cells

NOTE : EVERYTHING HAS TO BE KEPT ON ICE AND NO VORTEX

Throw competent cells on ice. Those can be prepared using the CaCl2 protocol
Place 20 µL of cells in a pre-chilled Eppendorf tube
For an intert vector, add 0,5 µL or less to the chilled cells
For a ligation product, add 2-3 µL to the chilled cells
Mix gently by flicking the tube
Chill on ice for 10 minutes - this step is optional but can improve yields when transforming a ligation product
Heat shock at 42°C for 30 seconds
Return on ice for 2 minutes
Add 200µL LB medium and recover the cells by shaking at 37°C
Another rich medium can substitute for the recovery. The recovery time varies with the antibiotic selection
Ampicillin : 15 - 30 minutes

Place out the cells on selective LB
Use glass beads to spread the cells. The volume of cells plated depends on what is being transformed

For an intact vector
High transformation efficiencies are expected. Plating out 10 µL of recovered cells should produce many colonies.

Note : 200 µL is the maximum volume of liquid that an LB plate can absorb
Incubate at 37°C. Transformants should appear within 12 hours

Conclusion
The BL 21 DE3 strain showed IP colonies
For the new NEB turbo cells, we see no colony
The old NEB turbo cells worked fine

Detect

Wednesday 17th of July

PCR purification

We are purifying the colony PCR from yesterday to send it away for sequencing

Procedure
Add 1.1 volume and Binding Buffer
Transfer up to 800 µL. Centrifuge for 30-60 seconds. Descend the flow through
Add 700 µL of washed Buffer. Centrifuge for 30-60 seconds
+ 1 min centrifuge to completely remove any residual wash buffer
Add 50 µL of Elution Buffer to the center of the Gene JT purification column membrane and centrifuge for 1 minute
Discard the Gene JET purification column and store the purified DNA at -20°C.

Detect

Thursday 18th July

Calculating the transformation efficiency for the E.coli NEB and E.coli NNEB strains.

· 20 µL of cell culture was inoculated in 200 µL of LB, where 0.5 µL of DNA sample (?) was added, giving the total volume of 220.5 µL.
· After the heat shock transformation 10 µL of the culture was diluted in 90 µL of LB, giving the 10-1 dilution (d); then 10 µL of this dilution was transferred in 90 µL of LB, giving the 10-2 dilution. 10 µL of each dilution (v) was plated on ampicillin media and left for incubation (24 h, 37 ̊C).


· After incubation, colonies were counted:
NEB NNEB
10-¹ 0 433
0 368
Average 0 400.5
10-¹ 0 62
0 40
Average 0 51

Obviously, NEB strain was not transformed and only NNEB was included in further calculations.
· The number of the transformed colony forming units per mL of the culture was calculated following the formula: colony number / d*v.

Calculation from the 10-1 dilution: 0.4 * 109 CFU/mL
Calculation from the 10-2 dilution: 0.51 * 109 CFU/mL

· The transformation efficiency was calculated by dividing the number of transformed colony forming units (CFU) by the amount of the DNA used (mDNA).

CFU1 = 0.4 * 109 CFU/mL * 0.22 mL (total V of the transformation culture) = 0.088*109 CFU
CFU2 = 0.51 * 109 CFU/mL * 0.22 mL = 0.1122*109 CFU

The concentration of the DNA solution which was used was 0.323 µg/µL, while the total DNA mass which was added to the transformation culture was: 0.323 µg/µL * 0.5 µL = 0.1615 µg.

So the transformation efficiency, calculated from the 10 times diluted (TE1) and 100 times diluted (TE2) cultures is:

TE1 = CFU1/mDNA = 0.55 * 109 CFU/µg
TE2 = CFU2/mDNA = 0.69 * 109 CFU/µg

TE1 and TE2 are almost the same

Detect

Monday 22nd July

Culture purification by streak plate method and preparing the glycerol stock for the sSP001 (TN 57) and sSP002 (NEC) strains.

Place your note here

Detect

Tuesday 23rd July

Colony PCR

· Strain: Keio ΔpyrF
· Primers: JW182 and JW183
· Amplified region: kanamycine resistance gene




Detect

Monday 29th July


Liquid culture of:
pCOLA DUET (from glycerol stock of Sabotage Group) - 20 ml culture
pSSB1 (from plate) - 5 ml culture
pSSB2 (from plate ) - 5 ml culture

Plating of addgene bacteria containing the plasmids we want:
streak out bacteria from addgene to get single colonies:
pBAC-BA-lacZ
pCRISPR
pCas9
pCRIPSR::rpsL

Detect

Tuesday 30th July

Liquid culture, Miniprep and Glycerol stock

Liquid culture of:
pCOLA DUET (from liquid culture (29.07.13)) - 20 ml culture
pSSB1 (from liquid culture (29.07.13)) - 5ml culture
pSSB2 (from liquid culture (29.07.13)) - 5 ml culture
pBAC-BA-lacZ (from plate ) - 5 ml culture
pCRISPR (from plate ) - 5 ml culture
pCas9 (from plate ) - 5 ml culture
pCRIPSR::rpsL (from plate ) - 5 ml culture
F+ strain - (from glycerol stock Sabotage) - 10 ml culture
Keio Keio delta pyrF (from plate ) - 10 ml culture


Miniprep (pCOLA-DUET = sSP007) using the Thermo Scientific Miniprep Kit

1) Pellet 2x9 ml of liquid culture (4000 rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250 µL of resuspension solution
4) add 250 µL of lysis solution, mix by inverting 4-6 times
5) add 350 µL of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 µL wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5 ml tube
11) add 50 µL of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

pSP001= pCOLA-DUET: 65 ng/ul



Glycerol Stock
from overnight culture of MG1655-pCOLA-DUET (sSP007)
Centrifuge 4000 rpm, 10 minutes,
take out liquid
resuspend cells in 0,5 mL glycerol (60%) , 2 mL LB
freeze in -80°C

Detect

Wednesday 31st July

Conjugation, Miniprep addgene plasmids,Glycerol Stock of addgene plasmids



Conjugation

sSP001, SP002, keio Delta PyrF
F+ comes from XL1 Blue (glycerol stock Sabotage) => F+ is tetR

Protocol :
1) From O/N cultures Dilute strains 1/100 in LB
2) Wait for OD to reach O,2
3) Prepare 4 tubes (in BD tubes) :
- Tube 1 = 0,5 mL LB with Strain 1 (sSP001) ,5 mL LB = control
- Tube 2 = 0,5 mL LB with Strain 2 (sP001) + 0,5 mL LB = control
- Tube 3 = 0,5 mL LB with Strain 3 (keio Delta pyrF) + 0,5 mL LB = control
- Tube 4 = 0,5 mL LB with Strain 4 (XL1) + 0,5 mL LB = control
- Tube 5 = 0,5 mL LB with Strain 1 (sSP001) + 0,5 mL LB with Strain 4 (XL1)
- Tube 6 = 0,5 mL LB with Strain 2 (sSP002) + 0,5 mL LB with Strain 4 (XL1)
- Tube 7 = 0,5 mL LB with Strain 3 (keio Delta pyrF) + 0,5 mL LB with Strain 4 (XL1)
4) Incubate 2 hours at 37°C (actually not in the shaker, but we accidently kept them in the shaker...)
5) Plate 10ul for controls, 100uL, 10ul for mixed tubes on LB antibiotics (Tube 5: Chl + Tet, Tube 6: Chl + Tet, Tube 7: Kan + Tet)
6) Incubate overnight at 37°C

Miniprep addgene plasmids
1) Pellet 4 ml of liquid culture (4000 rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250 µL of resuspension solution
4) add 250 µL of lysis solution, mix by inverting 4-6 times
5) add 350 µL of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 µL wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove leftover liquid
10) transfer the column on a 1.5 ml tube
11) add 50 µL of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

See Database for plasmid reference
pCas9:
pCRISPR:
pBac-LacZ:
pCRISPR::rpsL:

Glycerol Stock of addgene plasmids
(see Database for strain reference)
from overnight culture
Centrifuge 4000 rpm, 10 minutes,
take out liquid
resuspend cells in 0,5 mL glycerol (60%) , 2 mL LB
freeze in -80°C

Detect

Thursday 1st August

PCR (gradient + usual) of SPCR1, SPCR7, SPCR8, SPCR10, SPCR9, SPCR4

ReagentVolume
1x
Nuclease-free water37.25 µL
5x Phusion HF Buffer10 µL
10 mM dNTPs1 µL
Forward Primer (10 µM)0.5 µL
Reverse Primer (10 µM)0.5 µL
Template Plasmid0.25 µL
Phusion DNA Polymerase0.5 µL
Total Volume50 µL


Gradient:
Pos 1: 40°
Pos 2: 40,2°
Pos 3: 41,3°
Pos 4: 43,1°
Pos 5: 45,4°
Pos 6: 48°
Pos 7: 50,7°
Pos 8: 53,5°
Pos 9: 56,0°
Pos 10: 58,1°
Pos 11: 59,8°C
(Pos 12: 60,6°)

Usual PCR: 52°

Detect

Friday 2nd August

Place your twit here

Gels with PCR products: 1% Agar
100V 20 Min
10 min staining in BET







Detect

Monday 5th August

Place your twit here

5ml liquid culture with proper antibiotics of:
SSp001 + F+
sSP002 + F+
keio delta pyrF + F+

Gelelectrophoresis: 1% Agar, 100 V 20 min

Detect

Tuesday 6th August

Liquid cultures of sSP008-sSP0011

Detect

Wednesday 7th August

Glycerol Stock of sSP008-sSP0011, M13 Test, Single Colonies, Liquid cultures, PCR and Transformation


Glycerol Stock of sSP008-sSP0011
Take 1.5ml of ON culture + 500ul Glycerol (60%)
Freeze at -80°C

M13 Test
Plate from ON culture:
1) 1:1000 - sSP012: sSP009 (plate 200ul)
2) 200 ul sSP012
3) 200ul sSp009

Single Colonies
streak out ON culture of sSP012 to get single colonies

Liquid cultures of pir+ E.coli and pKD13 from Jake

PCR of SPCR4, SPCR7, SPCR8, SPCR9, SPCR10 from circuar backbone, directly taken from Biobrick plate

Protocol

ReagentVolume
1x
Nuclease-free water37,25µL
5x Phusion HF Buffer10µL
10 mM dNTPs1µL
Forward Primer (10 µM)0.5µL
Reverse Primer (10 µM)0.5µL
Template Plasmid0.25µL
Phusion DNA Polymerase0.5µL
Total Volume50µL


Thermocycler Protocol: NEB Phusion
TempTime
Start98°C30 secMelt
Cycle 198°C5 secMelt35 cycles
Cycle 240.5°C / 60°C25 secAnneal
Cycle 372°C30 sec per kbExtend
Finish72°C5 minExtend
Store10°CForeverStore


Transformation Biobricks BBa_K649304 (with pSB1C3 backbone) and BBa_J04450 (with pSB1A3 backbone) into NEB Turbo (heat shock trafo)

1) Thaw competent cells on ice.
2) Place 20 ul of cells in a pre-chilled Eppendorf tube.
3) Add 2.5 ul of plasmid (from Biobrick stock)
4) Mix gently by flicking the tube.
5) Chill on ice for 10 minutes.
4) Heat shock at 42 °C for 30 seconds
5) Return to ice for 2 minutes.
6) Add 200 ul LB medium and recover the cells by shaking at 37 °C.
Ampicillin: 15-30 minutes
Chloramphenicol: 60-120 minutes
7) Plate out the cells on selective LB (10ul)
8) Incubate at 37 °C. Transformants should appear within 12 hrs.


Result: BBa_J04450: many colonies, BBa_K649304 no colonies, plate rest

Detect

Thursday 8th August

Liquid culture of FR-433 (M13)

Gel of PCR products. 100V 20min 1%

4-7-8-9-10 (40.5°C)- 4-7-8-9-10 (60°C)

Detect

Friday 9th August

Liquid culture, Gel, Trafo of BBa_E1010 (pSB1C3 backbone) into NEB turbo, Glycerol Stock, Making electro competent cells of pir+ E.coli, Transforming pKD13 into pir+ E.coli, Miniprep NEB turbo with BBa-J04450:, Liquid culture and Patch plates.


Liquid culture
1:1000 from liquid: FR-433 (M13), 10 ml
pir+ E.coli: from plate, 25 ml
XL10: from plate 10 ml

Gel: rest of circular backbone PCR product, 1% Agar, 100V, 20 min
SPCR4-7-8-9-10 (40.5) SPCR4-7-8-9-10 (60.5)
Gel picture:
didn’t work

Trafo of BBa_E1010 (pSB1C3 backbone) into NEB turbo
1) Thaw competent cells on ice.
2) Place 20 µl of cells in a pre-chilled Eppendorf tube.
3) Add 2.5 µl of plasmid (from Biobrick stock)
4) Mix gently by flicking the tube.
5) Chill on ice for 10 minutes.
4) Heat shock at 42 °C for 30 seconds
5) Return to ice for 2 minutes.
6) Add 200 µl LB medium and recover the cells by shaking at 37 °C.
Chloramphenicol: 60-120 minutes
7) Plate out the cells on selective LB (10ul)
8) Incubate at 37 °C. Transformants should appear within 12 hrs.


Glycerol Stock FR-433 (M13) -> sSP012
Glycerol Stock pir+ -> sSP013
Glycerol Stock pKD13 -> sSP014
Glycerol Stock NEB turbo with BBa-J04450 -> sSP015
Take 1.5 ml of ON culture + 500ul Glycerol (60%)
Freeze at -80°C

Making electro competent cells of pir+ E.coli
Preparation of Electrocompetent Cells
Note: Competent cells should never be vortexed, as this will cause them to lyse and release salts into the media. Resuspend cells by pipetting up and down with a large pasteur pipet. Once they are chilled, cells should be continuously cold.

1) The night before the transformation, start an overnight culture of cells.
pir+ E.coli
2) The day of the transformation, dilute the cells 100X.
100 ml LB
Grow at 30°C for about 90 minutes.
3) When the cells reach an OD600 of 0.2.
4) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8.
Split the culture into 2x 50 ml falcon tubes, on ice.
Centrifuge at 4 °C for 10 min at 4000 rpm.
5) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 2x 25 ml of ice cold water.
Combine the volumes in a single 50 ml falcon tube.
6) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
7) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 µl of washed cells per transformation.

Transforming pKD13 into pir+ E.coli
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)

2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.

3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.

4) Preload a pipette with 1 ml of LB.

5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.

6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.

7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.

8) Incubate 2 h at 37 °C with shaking.

9) Plate 100 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.

10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.

Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.


Miniprep NEB turbo with BBa-J04450:
1) Pellet 2x 9 ml of liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250 µl of resuspension solution
4) add 250 µl of lysis solution, mix by inverting 4-6 times
5) add 350 µl of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 µl wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5 ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

J04450: 0ng/ul

Liquid culture of: sSP012
sSP008
sSP009
sSP010
sSP011
sSP001
sSP002
XL-10 = sSP016
sSP017= Litmus

Patch plates of:
sSP010
sSP013
sSP009s
sSP014
sSP012

Detect

Saturday 10th August

Test of M13 and Liquid culture

Test of M13

1) 100 μ l of plating bacteria per tube
2) Prepare tenfold serial dilutions (10-6 to 10-9 ) of the bacteriophage stock in LB
3) Put 10 μ l/ 100 μ l of each dilution to the bacteria
4) Mix the bacteriophage particles with the bacterial culture by vortexing gently.
5) Add 40 μ l of X-gal solution (working conc) and IPTG (working conc) solution to each of the tubes
6) Add 3ml of Agar to each tube and gently vortexing for 3 seconds
7) Pour the mixture onto plates containing LB medium supplemented with 5 mM MgCl2
8) Swirl the plate gently to ensure an even distribution of bacteria and agar.
9) Incubate them at 37°C.


Liquid culture:
E1010
J04550

Detect

Sunday 11th August

Patches of sSP001-sSP008, sSP015-18 and Stress experiment (Plate reader)

Patches of sSP001-sSP008, sSP015-18

Stress experiment (Plate reader)
sSP001, sSP002, sSP010, sSP011, sSP012 (M13)
1:1000 bacteria in M9 Glucose
Mitomycin C concentrations: 3,3*10^-3, 1,6*10°-3, 6,6*10°-4, 3,3*10°-4
Quadruplets of bacteria (+phage), Triplets of MMC

See also pipetting scheme in folder Experiments on Dropbox

On culture of FR-433, XL-10, delta pyrF
1:1000 culture at 30°

Detect

Monday 12th August

Glycerol Stock, Miniprep, M13 plate test, Patches

Glycerol Stock sSP018 - NEB with E1010
sSP017
sSP016
Take 1.5ml of ON culture + 500ul Glycerol (60%)
Freeze at -80°C

Miniprep
E1010
J04450

1) Pellet 2x 2ml of liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension olution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

J04450: ng/ul
E1010: ng/ul


M13 plate test
1) 100 μ l of plating bacteria per tube
2) Prepare tenfold serial dilutions (10-6 to 10-9 ) of the bacteriophage stock in LB
3) Put 10 μ l/ 100 μ l of each dilution to the bacteria
4) Mix the bacteriophage particles with the bacterial culture by vortexing gently.
5) Add 40 μ l of X-gal solution (working conc) and IPTG (working conc) solution to each of the tubes
6) Add 3ml of Agar to each tube and gently vortexing for 3 seconds
7) Pour the mixture onto plates containing LB medium supplemented with 5 mM MgCl2
8) Swirl the plate gently to ensure an even distribution of bacteria and agar.
9) Incubate them at 37°C.

Patches
check them and prepare new ones of those that haven’t been done yet

Detect

Tuesday 13th August

PCR circular and linear 40.5°C/ 60°C, Conjugation of XL-10 (with sSP011), Patches, Digestion M13 backbone, RFP insert and Gel of PCR

PCR circular and linear, 40.5°C, 60° of pSB1A3, pSB1C3

ReagentVolume
1x
Nuclease-free water37,25µL
5x Phusion HF Buffer10µL
10 mM dNTPs1µL
Forward Primer (10 µM)0.5µL
Reverse Primer (10 µM)0.5µL
Template Plasmid0.25µL
Phusion DNA Polymerase0.5µL
Total Volume50µL


Thermocycler Protocol: NEB Phusion
TempTime
Start98°C30 secMelt
Cycle 198°C5 secMelt35 cycles
Cycle 240.5°C / 60°C25 secAnneal
Cycle 372°C30 sec per kbExtend
Finish72°C5 minExtend
Store10°CForeverStore


Conjugation of XL-10 (with sSP011)
1) From O/N cultures Dilute strains 1/100 in LB
2) Wait for OD to reach O,2
3) Prepare tube (in BD tubes) :
- Tube = 0,5mL LB with Strain (sSP011) + 0,5mL LB with Strain (XL-10 Kan)
4) Incubate 2 hours at 37°C (actually not in the shaker, but we accidently kept them in the shaker...)
5) Plate 20ul for mixed tube on LB antiobiotics (Tet, Kan)
6) Incubate overnight at 37°C


Patches
check and make new ones


Digestion M13 backbone, RFP insert
for Backbone (M13mp18 plasmid): 3ug
7,58 ul plasmid (c=395ng/ul)
3 ul EcoRI
3 ul PstI
3ul 10x Fast Digest
13,42 ul H20
incubate for 12 min on 37°
heat inactivation: 80° 5 min
for insert (BBa_J04450): 5ug
31,4 ul plasmid
5 ul EcoRi
5 ul PstI
3,6 ul H20
incubate for 20 min at 37°
heat inactivation: 80° 5min

Gel of PCR (Amp 40.5 circ, lin, Chl 60° lin, circ)
100V, 20 min 1% gel




Detect

Wednesday 14th August

Gel of PCR, Gel of Digest, Gel Extraction, DpnI digest of PCR products, PCR purification

Gel of PCR (Amp 60° circ, lin, Chl 40.5 circ, lin) 100V, 20 min 1% gel

Gel of Digest
100V, 20 min 1% gel



Gel Extraction
Excise the DNA fragment from the agarose gel with a clean, sharp scalpel. Minimize the size of the gel slice by removing extra agarose.
Weigh the gel slice in a colorless tube. Add 3 volumes of Buffer QG to 1 volume of gel (100 mg ~ 100 μl). To help dissolve gel, mix by vortexing the tube every 2–3 min during the incubation.
After the gel slice has dissolved completely, check that the color of the mixture is yellow (similar to Buffer QG without dissolved agarose).
Add 1 gel volume of isopropanol to the sample and mix (actually only needed for very small products or very big products)
To bind DNA, apply the sample to the QIAquick column, and centrifuge for 1 min.
Discard flow-through and place QIAquick column back in the same collection tube.
To wash, add 0.75 ml of Buffer PE to QIAquick column and centrifuge for 1 min.
11. Discard the flow-through and centrifuge the QIAquick column for an additional 1 min at 17,900 x g (13,000 rpm). 12. Place QIAquick column into a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl elution buffer to the center of the QIAquick membrane, let the column stand for 1 min, and then centrifuge for 1 min.


DpnI digest of PCR products:
SPCR4 (40ul) - add 1 ul DpnI
SPCR 7 (150ul) - add 3 ul of DpnI
SPCR8 (60 ul) - add 3 ul of DpnI
SPCR 9 (150ul) - add 3 ul of DpnI
SPCR10 (110ul) - add 3 ul of DpnI
Incubate for 15 min at 37°C


PCR purification
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 50 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Detect

Thursday 15th August

Liquid cultures

Liquid cultures:
sSp009
sSP012
sSP016
sSp020
Xgal Bacteria from Aude

Detect

Friday 16th August

Liquid M13 Test, Glycerol Stock, Miniprep

Liquid M13 Test

OD (sSP020=XL10 KanR with F+)=0,557
OD (sSP016=XL10 KanR)=0,515
OD (sSP009= delta pyrF with F+)=0,561
OD(sSP012=FR-433=M13)=0,695

Prepare Falcons containing 500ul of each strain, adding 500ul of 10^-6 dilution of FR-433
add 1ul of IPTG and 1ul of Xgal
Incubate at 37° on shaker

Glycerol Stock sSP019 (pir+ E.coli transformed with pKD13)
sSP020 (XL10 KanR with F+)

Miniprep
sSP019
sSP017

1) Pellet 2x 2ml of liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension olution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

pKD13: 311ng/ul
Litmus 28i: 93ng/ul

Detect

Monday 19th August

Restreak XL-1 Blue Litmus28i, PCR, PCR purification Backbone (M13mp18), Ligation (RFP into M13mp18 backbone), Trafo of Ligation product (RFP in M13mp18 plasmid) into NEB turbo and Test Xgal

Restreak XL-1 Blue Litmus28i

PCR

SPCR5, SPCR6, 49,3°C

ReagentVolume
1x
Nuclease-free water37,25µL
5x Phusion HF Buffer10µL
10 mM dNTPs1µL
Forward Primer (10 µM)0.5µL
Reverse Primer (10 µM)0.5µL
Template Plasmid0.25µL
Phusion DNA Polymerase0.5µL
Total Volume50µL


Thermocycler Protocol: NEB Phusion
TempTime
Start98°C30 secMelt
Cycle 198°C5 secMelt35 cycles
Cycle 240.5°C / 60°C25 secAnneal
Cycle 372°C30 sec per kbExtend
Finish72°C5 minExtend
Store10°CForeverStore


PCR purification Backbone (M13mp18)
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 50 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Ligation (RFP into M13mp18 backbone)
3ul Backbone
14 ul Insert
2ul 10x T4 DNA Ligase HC Buffer
1 ul T4 DNA Ligase

Incubate for at least 10min at 22°C


Trafo of Ligation product (RFP in M13mp18 plasmid) into NEB turbo
1) Thaw competent cells on ice.
2) Place 20 ul of cells in a pre-chilled Eppendorf tube.
3) Add 3 ul of plasmid (from Biobrick stock)
4) Mix gently by flicking the tube.
5) Chill on ice for 10 minutes.
4) Heat shock at 42 °C for 30 seconds
5) Return to ice for 2 minutes.
6) Add 200 ul LB medium and recover the cells by shaking at 37 °C.
7) Plate out the cells on LB (200ul)
8. Incubate at 37 °C. Transformants should appear within 12 hrs.

Test Xgal
3ml of Liquid culture with
1) Xgal from iGEM 2012 (Jake) (+IPTG)
2) Xgal from last week (in DMF) (+IPTG)

Detect

Tuesday 20th August

Gel of PCR and Xgal Test

Gel of PCR

1%, 100V, 20min



Result: PCR didn’t work


Xgal Test

MG1655 (of Jake) in liquid culture with Xgal of iGEM 2012, Aude and new one (Anne)

Result:
All cultures turn blue (Aude, less blue)

Detect

Wednesday 21st August

Gradient PCR SPCR5, SPCR6, M13 Test, Electrocompetent Cells (sSP017-XL-1 Blue, Litmus 28i), Transformation

Gradient PCR SPCR5, SPCR6

ReagentVolume
1x
Nuclease-free water37,25µL
5x Phusion HF Buffer10µL
10 mM dNTPs1µL
Forward Primer (10 µM)0.5µL
Reverse Primer (10 µM)0.5µL
Template Plasmid0.25µL
Phusion DNA Polymerase0.5µL
Total Volume50µL


Gradient:
Pos 1: 40.1°
Pos 2: 40,8°
Pos 3: 42.2°
Pos 4: 44.2°
Pos 5: 46.7°
Pos 6: 49.4°
Pos 7: 52.1°
Pos 8: 54.7°
Pos 9: 57.1°
Pos 10: 59.0°
Pos 11: 60.2°C

M13 Test
Liquid cultures of sSP012 and sSP020
1) 100 μ l of plating bacteria per tube
2) Prepare tenfold serial dilutions (10-6 to 10-9 ) of the bacteriophage stock in LB
3) Put 10 μ l/ 100 μ l of each dilution to the bacteria
4) Mix the bacteriophage particles with the bacterial culture by vortexing gently.
5) Add 40 μ l of X-gal solution (working conc) and IPTG (working conc) solution to each of the tubes
6) Add 3ml of Agar to each tube and gently vortexing for 3 seconds
7) Pour the mixture onto plates containing LB medium supplemented with 5 mM MgCl2
8) Swirl the plate gently to ensure an even distribution of bacteria and agar.
9) Incubate them at 37°C.


Electrocompetent Cells (sSP017-XL-1 Blue, Litmus 28i)
1) The night before the transformation, start an overnight culture of cells.
sSP017 (XL1 Blue Litmus 28i)
2) The day of the transformation, dilute the cells 100X.
100 ml LB Amp.
Grow at 30°C for about 90 minutes.
3) When the cells reach an OD600 of 0.2.
4) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
Split the culture into 2x 50 ml falcon tubes, on ice.
Centrifuge at 4 °C for 10 min at 4000 rpm.
5) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 2x 25 ml of ice cold water.
Combine the volumes in a single 50 ml falcon tube.
6) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
7) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.

Transforming pKD13 into pir+ E.coli
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)

2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.

3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.

4) Preload a pipette with 1 ml of LB.

5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.

6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.

7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.

8) Incubate 2 h at 37 °C with shaking.

9) Plate 100 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.

10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.

Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.

Detect

Thursday 22nd August

Gel of gradient PCR product (Pictures 6,5,5), PCR purification and pooling, Digestion M13 backbone, RFP insert, Test Digestion in Gel, Gel Extraction, Liquid culture, Purification of Backbone Cloning and Miniprep sSP015.


Gel of gradient PCR product
1%, 100V, 20 min







PCR purification and pooling
Pool all samples that worked
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 50 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

c(SPCR5)= ng/ul
c(SPCR6)= ng/ul


Digestion M13 backbone, RFP insert

Backbone/Insert (double the amount)

RegentVolume
Purified Plasmid20 ul
H2O65 ul
10x FastDigest Buffer10 ul
FastDigest Enzyme 1 (EcoRI)2,5 ul
FastDigest Enzyme 2 (PstI)2,5 ul
FastAP Phosphatase0 ul
Total Volume100ul

Digest for 2.5 hours at 37 °C with shaking.


Test Digestion in Gel
1%, 100V, 20 min

Gel Extraction
Excise the DNA fragment from the agarose gel with a clean, sharp scalpel. Minimize the size of the gel slice by removing extra agarose.
Weigh the gel slice in a colorless tube. Add 3 volumes of Buffer QG to 1 volume of gel (100 mg ~ 100 μl). To help dissolve gel, mix by vortexing the tube every 2–3 min during the incubation.
After the gel slice has dissolved completely, check that the color of the mixture is yellow (similar to Buffer QG without dissolved agarose).
Add 1 gel volume of isopropanol to the sample and mix (actually only needed for very small products or very big products)
To bind DNA, apply the sample to the QIAquick column, and centrifuge for 1 min.
Discard flow-through and place QIAquick column back in the same collection tube.
To wash, add 0.75 ml of Buffer PE to QIAquick column and centrifuge for 1 min.
11. Discard the flow-through and centrifuge the QIAquick column for an additional 1 min at 17,900 x g (13,000 rpm). 12. Place QIAquick column into a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl elution buffer to the center of the QIAquick membrane, let the column stand for 1 min, and then centrifuge for 1 min.

c=13,6ng/ul

Liquid culture
sSP015

Purification of Backbone Cloning
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Miniprep sSP015
1) Pellet 2x 2ml of liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension solution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

Detect

Friday 23rd August

Stress Experiment (sSP001, sSP002, sSP010, sSP011, M13, MMC), Microscope, Gradient PCR of SPCR2, Digestion of SPCR 5 and SPCR7 and Purification of Digestion.

Stress Experiment (sSP001, sSP002, sSP010, sSP011, M13, MMC)
Dilute ON culture 1:100
Centrifuge (1 min, 10rpm)
Wash 1x with 70% of Volume M9 Glucose
Centrifuge again
Take up in 70% of the VOlume M9 Gluo
100ul in each 96 well plate (see pipetting file)
Add MMC 10ug/ml in corresponding wells and incubate in the plate reader
After 90 min add phages into correscponding wells
put back on the plate reader

Microscope
look at the shape and fluorescence at t=0 of sSP001
look at the shape and fluorescence at=90 mi of sSP001 + 10ug/ml MMC
take photos


Gradient PCR of SPCR2
iSP001 (gblock) and iS002

ReagentVolume
1x
Nuclease-free water37,25µL
5x Phusion HF Buffer10µL
10 mM dNTPs1µL
Forward Primer (10 µM)0.5µL
Reverse Primer (10 µM)0.5µL
Template Plasmid0.25µL
Phusion DNA Polymerase0.5µL
Total Volume50µL


Thermocycler Protocol: NEB Phusion
TempTime
Start98°C30 secMelt
Cycle 198°C5 secMelt35 cycles
Cycle 240.5°C / 60°C25 secAnneal
Cycle 372°C30 sec per kbExtend
Finish72°C5 minExtend
Store10°CForeverStore


Digestion of SPCR 5 and SPCR7
ReagentVolume
Purified PCR Product16 ul
H2O0 ul
10x FastDigest Buffer2 ul
FastDigest Enzyme 11 ul
FastDigest Enzyme 21 ul
Total Volume20 ul
Incubate at 37°C for 1h shaking


Purification of Digestion
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Detect

Sunday 25th August

Gel of Gradient PCR, Liquid Cultures, Ligation M13 + RFP, Ligation SPCR5, SPCR7, Electrocompetent cells, Gibson Assembly, Transformation (Gibson)and Transformation (Gibson, Ligations.

Gel of Gradient PCR
1%, 100V, 20min



Liquid Cultures
NEB Turbo
XL10

Ligation

Ligation M13 + RFP
0.5ul Vector (M13)
2.6ul Insert (RFP)
5.4ul H20
1.0ul T4 buffer
0.5ul T4 Ligase

Ligation SPCR5, SPCR7
1.0ul Vector (SPCR5)
1.5ul Insert (SPCR7)
6.0ul H20
1.0ul T4 buffer
0.5ul T4 Ligase

Incubate ~30min at 37 C

Electrocompetent cells
1) Start Culture
2) When the cells reach an OD600 of 0.2.
3) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
Centrifuge at 4 °C for 10 min at 4000 rpm.
4) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 25 ml of ice cold water
5) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat. 6) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.

Gibson Assembly

Amount per Reaction
Positive Control**

PCR Fragment(s)
+ linearized vector
2-10 μl (0.02–0.5 pmols)*

Gibson
Assembly Master
Mix (2X)
10 μl

Deionized H2O
XX μl

Total Volume
20 μl

Incubate samples in a thermocycler at 50°C for 15 minutes. After incubation, store the samples on ice or at -20°C for subsequent transformation
Note: Extended incubation up to 60 minutes may help to improve assembly efficiency in some cases (for further details see FAQ section).
Transform NEB 5-alpha Competent E. coli cells (provided with the kit) with 2 μl of the assembly reaction, following the transformation protocol.

Transformation (Gibson)
Thaw competent cells on ice.
Add 2 μl of the chilled assembly product to the competent cells. Mix gently by pipetting up and down or by flicking the tube 4–5 times. Do not vortex.
Place the mixture on ice for 30 minutes. Do not mix.
Heat shock at 42°C for 30 seconds. Do not mix.
Transfer tubes to ice for 2 minutes.
Add 950 μl of room-temperature SOC media to the tube.
Incubate the tube at 37°C for 60 minutes. Shake vigorously (250 rpm) or rotate.
Warm selection plates to 37°C.
Spread 100 μl of the cells onto the selection plates. Use Amp plates for positive control sample.
Incubate overnight at 37°C.

Transformation (Gibson, Ligations)
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)

2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.

3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.

4) Preload a pipette with 1 ml of LB.

5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.

6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.

7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.

8) Incubate 2 h at 37 °C with shaking.

9) Plate 100 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.

10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.

Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.

Detect

Monday 26th August


Picking colonies (Trafo Gibson, BBC SPCR5/7)
chosing 5-7 colonies and start liquid cultures

Detect

Tuesday 27th August

Starting liquid cultures and Miniprep of pS.005 and pS.006.

Starting liquid cultures
sSP001, sSP002, sSP010, sSP011, sSP012, sSP020

Miniprep of pS.005 and pS.006
1) Pellet 2x 9ml of liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension solution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

Colony PCR

ReagentVolume
Forward Primer (10 uM)0,5 ul
Reverse Primer (10 uM)0,5 ul
Template DNA (Miniprep)0,5 ul
Quick-Load® Taq 2X Master Mix12,5 ul
Nuclease-free water10,0 ul
Total volume25 ul

Thermocycler Protocol: Dream Taq Green
Temp Time
Start 95°C 30 sec1 Melt
Cycle 1 95°C 15 sec Melt 35 cycles
Cycle 2 46,8°C 30 sec Anneal
Cycle 3 68°C 1 min per kb Extend cellule 2
Finish 68°C 5 min Extend
Store 10°C Forever Store

Detect

Wednesday 28th August

Gel Colony PCR, Liquid Cultures (1:100), Analytical Digest, Gel Ligation/Gibson, Gel Analytical digest, DpnI digest of SPCR5, SPCR6, SPCR7, Gel DpnI digest, PCR purification of DpnI digested SPCR5, SPCR6, SPCR7, Stress test microscope and M13 Test.

Gel Colony PCR
pS005 (C1-C5) - pS006 (C1-C7)
1% 100V 20 min


Liquid Cultures (1:100)
sSP001, sSP002, sSP010, sSP011, sSP012, sSP020

Analytical Digest

ReagentVolume
Plasmid Miniprep 5 ul
H2O12 ul
c10x FastDigest Buffer2ul
FastDigest Enzyme 10,5 ul
FastDigest Enzyme 20,5 ul
Total Volume 20,0 ul
Digest for 15 minutes at 37 °C with shaking


Gel Ligation/Gibson
pS005 - pS006 - M13/RFP
1% 100V 20min



Gel Analytical digest
pS005 (C1-C5)-pS006 (C1-C7)
1% 100V 20min



DpnI digest of SPCR5, SPCR6, SPCR7
add 4ul of DpnI into each tube, mix and incubate for 1h at 37°C

Gel DpnI digest
let each 5ul run on a gel
1%, 100V 20min

PCR purification of DpnI digested SPCR5, SPCR6, SPCR7
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Stress test microscope
Dilute ON cultures of sSP001, sSP002, sSP010, sSP011, sSP012 1:100 and incubate up to an OD of 0.3
Take out 2ml of sSP001, sSP002, sSP010, sSP011
add:
sSP001: 10ug/ml MMC
sSP002: 10ug/ml MMC
sSP010: 20ul sSP012 supernatant
sSP011: 20ul sSP012 supernatant

incubate for 90 min

take pictures under the microscope (trans and YFP) of (un-)treated samples


M13 Test
Liquid cultures of sSP012 and sSP020
1) 100 μ l of plating bacteria per tube (OD 0.6)
2) Prepare tenfold serial dilutions (10-6 to 10-9 ) of the bacteriophage stock in LB
3) Put 10 μ l/ 100 μ l of each dilution to the bacteria
4) Mix the bacteriophage particles with the bacterial culture by vortexing gently.
5) Add 40 μ l of X-gal solution (working conc) and IPTG (working conc) solution to each of the tubes
6) Add 3ml of Agar to each tube and gently vortexing for 3 seconds
7) Pour the mixture onto plates containing LB medium supplemented with 5 mM MgCl2 and 2x IPTG and Xgal
8) Swirl the plate gently to ensure an even distribution of bacteria and agar.
9) Incubate them at 37°C.

Detect

Friday 30th August

M13 test, DpnI digest (SPCR5,6,7), Gel SPCR5,6,7 and PCR purification of DpnI digested SPCR5, SPCR6, SPCR7

M13 test
dilute ON cultures (NEB turbo, FR-433) 1: 100, grow up to an OD of ~0.6
1) 100 μ l of plating bacteria per tube (OD 0.6)
2) Prepare tenfold serial dilutions (10-6 to 10-9 ) of the bacteriophage stock in LB
3) Put 10 μ l/ 100 μ l of each dilution to the bacteria
4) Mix the bacteriophage particles with the bacterial culture by vortexing gently.
5) Add 40 μ l of X-gal solution (working conc) and IPTG (working conc) solution to each of the tubes
6) Add 3ml of Agar to each tube and gently vortexing for 3 seconds
7) Pour the mixture onto plates containing LB medium supplemented with 5 mM MgCl2 and 2x IPTG and Xgal
8) Swirl the plate gently to ensure an even distribution of bacteria and agar.
9) Incubate them at 37°C.

DpnI digest (SPCR5,6,7)
add 8ul DpnI per tube and digest for 1h at 37°, shaking

Gel SPCR5,6,7
1%, 100V, 20min


PCR purification of DpnI digested SPCR5, SPCR6, SPCR7
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Detect

Day Numbersuffix Month

Place your twit here

Place your note here

Detect

Wednesday 4th September

Starting Liquid culture, PCRs, Gel, DpnI digest, Digestion of SPCR5,7, Purification of Digestion, Ligation of SPCR5,7, Gibson Assembly, Making Electrocompetent Cells, Transformation, Redo SPCR12/13 ,

Starting Liquid culture
NEB turbo, grow up to an OD of 0.6

PCRs
SPCR1, SPCR2, SPCR4, SPCR12, SPCR13

Reagant Volume
1x (SPCR2) 11x (SPCR12) 11x (SPCR13) 8x (SPCR1) 8x (SPCR4)
Nuclease-free water 37.25 µl 447 µl 447 µl 335,25µl 335,25µl
5x Phusion HF Buffer 10 µl 120 µl 120 µl 90 µl 90 µl
10 mM dNTPs 1 µl 12 µl 12 µl 9 µl 9 µl
Forward Primer (10 uM) 0.5 µl 6 µl 6 µl 4.5 µl 4.5 µl
Reverse Primer (10 uM) 0.5 µl 6 µl 6 µl 4.5 µl 4.5 µl
Template Plasmid 0.25 µl 3 µl 3 µl 2.25 µl 2.25 µl
Phusion DNA Polymerase 0.5 µl 6 µl 6 µl 4,5 µl 4,5 µl
Total Volume 50 µl 600 µl 600 µl 450 µl 450 µl


for SPCR 12/13 gradient, 2,5 min
for SPCR3, SPCR11 51°, 45s
for SPCR 1, SPCR2, 48,8°, 2 min
for SPCR4, 40,8°, 1 min

Gel
1%, 100V, 20 min

1.small gel (SPCR1,2,3,4,11)
2. big gel (SPCR12)
3. big Gel (SPCR13)







DpnI digest
SPCR 1: add 10ul DpnI
SPCR4: add 10ul DpnI
SPCR2,3,11: add 1 ul DpnI

incubate for 1h at 37°

Digestion of SPCR5,7

Reagent Volume
Purified PCR Product 16 µl
H2O 0 µl
10x FastDigest Buffer 2 µl
XbaI 1 µl
SpeI 1 µl
Total Volume 20.0 µl

Incubate for 1h at 37°, shaking

Purification of Digestion
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 30 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Ligation of SPCR5,7

Reagent Volume
Vector 1 µl
Insert 3 µl
H2O 4.5 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl

Incubate at room temperature for ~1h

Gibson Assembly

Amount per Reaction : Positive Control**

PCR Fragment(s)+ linearized vector : 2-10 μl (0.02–0.5 pmols)*

Gibson Assembly Master Mix (2X): 10 μl

Deionized H2O : XX μl

Total Volume : 20 μl

Incubate samples in a thermocycler at 50°C for 15 minutes.
Put on Ice
Insert: 2,4 ul
Vector: 0,6 ul

Making Electrocompetent Cells

1) Start a liquid culture of cells. NEB turbo
2) dilute the cells 100X.
100 ml LB.
Grow at 30°C for about 90 minutes.
3) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8
Split the culture into 2x 50 ml falcon tubes, on ice.
Centrifuge at 4 °C for 10 min at 4000 rpm.
5) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 2x 25 ml of ice cold water.
Combine the volumes in a single 50 ml falcon tube.
6) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
7) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.

Transformation
pS005, pS006, SPCR3 (IDT plasmid) M13mp18
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)

2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.

3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.

4) Preload a pipette with 1 ml of LB.

5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.

6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.

7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.

8) Incubate 2 h at 37 °C with shaking.

9) Plate 10/200 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.

10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.

Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.

Redo SPCR12/13
Reagent Volume
11x (SPCR12) 11x (SPCR13)
Nuclease-free water 447 µl 447 µl
5x Phusion HF Buffer 120 µl 120 µl
10 mM dNTPs 12 µl 12 µl
Forward Primer (10 uM) 6 µl 6 µl
Reverse Primer (10 uM) 6 µl 6 µl
Template Plasmid 3 µl 3 µl
Phusion DNA Polymerase 6 µl 6 µl
Total Volume 600 µl 600 µl


Cycling protocol as usual + gradient + topdown

Detect

Thursday 5th September

Gel, Colony PCR, Topdown PCR and gels

Gel
SPCR12, SPCR13
1%, 100V, 20 min

Pictures: 13/09/05_SPCR12_corresponding primers


13/09/05_SPCR13_corresponding primers



Colony PCR

Reagent Volume
Forward Primer (10 uM)/td> 0.5 ul
Reverse Primer (10 uM) 0.5 ul
Template DNA (from above) 1.5 ul
Quick-Load® Taq 2X Master Mix 12.5 ul
Total Volume 25 ul

Thermocycler Protocol: DreamTaq Green PCR MM
Temp Time
Start 95°C 1 min Melt
Cycle 1 95°C 30 sec Melt 35 cycles
Cyle 2 52.6/46.8 °C 30 sec Anneal
Cycle 3 72°C 1 min per kb Extend
Finish 72°C 10 min Extend
Store 10°C Forever Store

Topdown PCR
SPCR 1,4,12,13

Reagent Volume
x1>/b>
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 0.5 µl
Reverse Primer (10 uM) 0.5 µl
Template Plasmid 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl

increases every cycle 1°C, starting from 40°


Gels
1%, 100V, 20+ Min

Pictures:
13/09/05_colony PCR_pS005_C1-C8_BB verification primers


13/09/05_colony PCR_pS005_C9-C16_BB verification primers


13/09/05_colony PCR_pS006_C1-C8_BB verification primers


13/09/05_colony PCR_pS006_C9-C16_BB verification primers


13/09/05_top down PCR_SPCR1,4,12,13


Detect

Friday 6th September

Place your twit here

Digestions: linearized pSB1C3, linearized pSB1A3, SPCR2, SPCR3, SPCR11

Reagent Volume
Purified PCR Product 16 µl
H2OH2O 0 µl
10x FastDigest Buffer 2 µl
FastDigest Enzyme 1 1 µl
cFastDigest Enzyme 2 1 µl
Total Volume 4 µl


SPCR5, pSB1C3: XbaI/SpeI
SPCR11, pSB1A3, pSB1C3: EcoRI/PstI
SPCR13, pSB1A3, pSB1C3: EcoRI/PstI
SPCR2, pSB1A3, pSB1C3: EcoRI/PstI

1h at 37° shaking

Detect

Saturday 7th September

Ligation, Making Electrocompetent Cells, Gibson Assembly, Transformation, Liquid culture of E1010

Ligation

Reagent Volume
Vector 1 µl
Insert 3 µl
H2O 4.5 µl
Fermentas T4 Ligase Buffer 1
Fermentas T4 Ligase Enzyme 0.5
Total Volume 10 µl


SPCR5, pSB1C3
SPCR11, pSB1A3, pSB1C3
SPCR13, pSB1A3, pSB1C3
SPCR2, pSB1A3, pSB1C3

Incubate at room temperature for 10 minutes.


Making Electrocompetent Cells
1) Start a liquid culture of cells.
NEB turbo
2) dilute the cells 100X.
100 ml LB.
Grow at 30°C for about 90 minutes.
3) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8
Split the culture into 2x 50 ml falcon tubes, on ice.
Centrifuge at 4 °C for 10 min at 4000 rpm.
5) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 2x 25 ml of ice cold water.
Combine the volumes in a single 50 ml falcon tube.
6) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
7) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.



Gibson Assembly

Amount per Reaction
Positive Control**


PCR Fragment(s)
+ linearized vector
2-10 μl (0.02–0.5 pmols)*


Gibson
Assembly Master
Mix (2X)
10 μl


Deionized H2O
XX μl

Total Volume
20 μl



Incubate samples in a thermocycler at 50°C for 15 minutes.
Put on Ice


Transformation pS002 (Chl), pS002 (Amp), pS003 (Amp), pS004 (Chl), pS004 (Amp), pS005 (Chl), pS006-7 (Chl), pS007 (Chl), pS008 (Amp), pS009 (Chl), pS012 (Amp), pS013 (Chl), pS013 (Amp)

1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)

2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.

3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.

4) Preload a pipette with 1 ml of LB.

5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.

6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.

7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.

8) Incubate 1/2 h at 37 °C with shaking.

9) Plate 10/200 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.

10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.

Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.

Liquid culture of E1010

Detect

Sunday 8th September

Replating of transformation and Miniprep of E1010

Replating of Transformation

Miniprep of E1010
1) Pellet liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension olution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

Detect

Monday 16th September

Result Cloning, Protocol: E. coli Colony PCR, Extraction of DNA, PCR Reaction and Gels

Result Cloning:
Colonies?
pS002 (Chl): no
pS002 (Amp): yes
pS003 (Amp):yes
pS004 (Chl): no
pS004 (Amp): yes
pS005 (Chl): yes
pS006-7 (Chl): yes
pS006 (Chl): no
pS007 (Chl): yes
pS008 (Amp): yes
pS009 (Chl): yes
pS012 (Amp): yes
pS013 (Chl): no
pS013 (Amp): yes

Protocol: E. coli Colony PCR
Using the Dream Taq Master Mix

Extraction of DNA

1) Pick a single colony into 50 ul of H20.

2) Boil for 5 minutes.

PCR Reaction (pS002 (Chl-Lig), pS005 (Chl-G), pS006-7 (Chl-Lig), pS007 (Chl-G), pS008 (Amp-G), pS009 (Chl-G))

Keep all the reagents at 4 °C while preparing the mixture.
Pre-heat the thermocycler to 95 °C and transfer your reaction directly from 4 °C.


Reagent Volume
Forward Primer (10 uM) 0.5 ul
Reverse Primer (10 uM) 0.5 ul
Template DNA (from above) 1.5 ul
Quick-Load® Taq 2X Master Mix 12.5 ul
Nuclease-free water 10 ul
Total Volume 25 ul



Thermocycler Protocol: NEB Quick-Load
Temp Time
Start 95°C 30 sec Melt
Cycle 1 95°C 15 sec Melt 35 cycles
Cycle 2 45.8 °C 30 sec Anneal
Cycle 3 72°C 1 min per kb Extend
Finish 72 °C 15 min Extand
Store 10°C Forever Store



Gels
100V, 25-30 min, 1%

Pictures:
13/09/16_colony PCR_ps007.BMP


13/09/16_colony PCR_pS006-7.BMP


13/09/16_colony PCR_ps005.BMP



Result: didn’t work

Detect

Tuesday 17th September

PCR Reaction (pS003 (Amp-G), pS004 (Amp-Lig), pS012 (Amp-G), pS013 (Chl-Lig))

PCR Reaction (pS003 (Amp-G), pS004 (Amp-Lig), pS012 (Amp-G), pS013 (Chl-Lig))

Keep all the reagents at 4 °C while preparing the mixture.
Pre-heat the thermocycler to 95 °C and transfer your reaction directly from 4 °C.

Reagent Volume
Forward Primer (10 uM) 0.5 ul
Reverse Primer (10 uM) 0.5 ul
Template DNA (from above) 1.5 ul
Quick-Load® Taq 2X Master Mix 12.5 ul
Nuclease-free water 10 ul
Total Volume 25 ul



Thermocycler Protocol: NEB Quick-Load
Temp Time
Start 95°C 30 sec Melt
Cycle 1 95°C 15 sec Melt 35 cycles
Cycle 2 45.8 °C 30 sec Anneal
Cycle 3 72°C 1 min per kb Extend
Finish 72 °C 15 min Extand
Store 10°C Forever Store




Gels
100V, 30 min, 1%

Pictures: 13/09/17_colony PCR_pS009.JPG


13/09/17_colony PCR_pS008_pS002.jpg


13/09/17_colony PCR_pS003.JPG


13/09/17_colony PCR_pS004.JPG


13/09/17_colony PCR_pS012.JPG


13/09/17_colony PCR_pS013.JPG



Result:
pS003: row 3,5 might have worked -> analytical digest
pS004: all might have worked -> analytical digest
pS013: all might have worked -> analytical digest
pS012: row 3,4,5 might have workes -> analytical digest

Sequencing
Bringing primers/plasmids away for sequencin
Bacbbone, SPCR2 with iS002, iS032, iS028, iS029, iS030

Detect

Wednesday 16th September

Ligations

Ligation

SPCR2 - Chl

Reagent Volume
SPCR2 1 µl
Chl 2,95 µl
H2O 4.55 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


SPCR2 - Amp

Reagent Volume
SPCR2 1 µl
Amp 3.4 µl
H2O 4.1 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


SPCR3 - Chl

Reagent Volume
SPCR3 1 µl
Amp 1.79 µl
H2O 5.71 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


SPCR3 - Amp7
Reagent Volume
Amp 1 µl
SPCR 3 1.56 µl
H2O 5.94 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


SPCR5 - Chl

Reagent Volume
SPCR 5 0.5 µl
Chl 4.55 µl
H2O 3.45 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


SPCR11 - Chl

Reagent Volume
Chl 1 µl
SPCR11 1.3 µl
H2O 6.2 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


SPCR2 - Amp
Reagent Volume
Amp 1 µl
SPCR11 1.13 µl
H2O 6.37 µl
Fermentas T4 Ligase Buffer 1.0 µl
Fermentas T4 Ligase Enzyme 0.5 µl
Total Volume 10 µl


at 16° for 1h

Transformation
1) Thaw competent cells on ice (Gibson Kit competent cells)
2) Place 20 ul of cells in a pre-chilled Eppendorf tube.
3) Add 2.5 ul of plasmid (from Biobrick stock)
4) Mix gently by flicking the tube.
5) Chill on ice for 10 minutes.
4) Heat shock at 42 °C for 30 seconds
5) Return to ice for 2 minutes.
6) Add 200 ul LB medium and recover the cells by shaking at 37 °C.
Ampicillin: 15-30 minutes
Chloramphenicol: 60-120 minutes
7) Plate out the cells on selective LB (10ul)
8. Incubate at 37 °C. Transformants should appear within 12 hrs.

Gel of Ligation products
1%, 100V, 40 min

Detect

Sunday 22nd September

PCR and Gels

PCR
M13 backbone

SPCR16,17

Reagent Volume
x1
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 0.5 µl
Reverse Primer (10 uM) 0.5 µl
Template Plasmid 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl

Protocol see fotos

Gel 100V, 1%, 1,5h

Detect

Monday 23rd September

Gels and PCR

Gel
100V, 1%, 1,5h

Picture: 13/09/23_SPCR16_17_corresponding primers - PCRs didn't worked


PCR
SPCR 16 (normal phusion at 48°C)

Reagent Volume
x1
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 0.5 µl
Reverse Primer (10 uM) 0.5 µl
Template Plasmid 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl



Thermocycler Protocol: NEB Phusion
Temp Time
Start 98°C 30 sec Melt
Cycle 1 98°C 5 sec Melt 35 cycles
Cycle 2 72°C 30 sec Anneal
Cycle 3 72°C 30 sec per kb Extend
Finish 72 °C 5 min Extand
Store 10°C Forever Store



Detect

Tuesday 24th September

Overlap PCR, PCR of Overlap, Digestion, Gel extraction, Gels, PCR Purification, PCR (SPCR2, SPCR3, SPCR5, SPCR6, SPCR7, SPCR8, SPCR9, SPCR10, SPCR11, linearize pSB1C3) and liquid culture

Overlap PCR
SPCR5-SPCR2

Reagent Volume
x1
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Template Plasmid(10 uM) 1 µl
Template Plasmid (10 uM) 1 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl






PCR of Overlap

Digestion
M13 (EcoRI, PstI), pSB1C3 (EcoRI, PstI), psB1C3 (XbaI, SpeI)

Reagent Volume
Purified Plasmid 20 µl
H2O 63 µl
10x FastDigest Buffer 10 µl
FastDigest Enzyme 1 2.5 µl
FastDigest Enzyme 2 2.5 µl
FastAP Phosphatase 2 µl
Total Volume 100 µl


SPCR2 (EcoRI, PstI), SPCR5 (XbaI, SpeI)

Reagent Volume
Purified PCR Product 16 µl
H2O 0 µl
10x FastDigest Buffer 2 µl
FastDigest Enzyme 1 1 µl
FastDigest Enzyme 2 1 µl
Total Volume 20 µl


Gel
pSB1C3
1%, 100V, 1h
Picture: 13/09/24_pSB1C3 digest_EcoRI/PstI_XbaI/SpeI - digest worked



Gel extraction
1. Excise the DNA fragment from the agarose gel with a clean, sharp scalpel. Minimize the size of the gel slice by removing extra agarose.
2. Weigh the gel slice in a colorless tube. Add 3 volumes of Buffer QG to 1 volume of gel (100 mg ~ 100 μl). To help dissolve gel, mix by vortexing the tube every 2–3 min during the incubation.
3. After the gel slice has dissolved completely, check that the color of the mixture is yellow (similar to Buffer QG without dissolved agarose).
4. Add 1 gel volume of isopropanol to the sample and mix (actually only needed for very small products or very big products) 5. To bind DNA, apply the sample to the QIAquick column, and centrifuge for 1 min.
6. Discard flow-through and place QIAquick column back in the same collection tube.
7. To wash, add 0.75 ml of Buffer PE to QIAquick column and centrifuge for 1 min.
8. Discard the flow-through and centrifuge the QIAquick column for an additional 1 min at 17,900 x g (13,000 rpm).
9. Place QIAquick column into a clean 1.5 ml microcentrifuge tube.
10. To elute DNA, add 30 μl elution buffer to the center of the QIAquick membrane, let the column stand for 1 min, and then centrifuge for 1 min.

Gel
PCR Overlap
1%, 100V, 1h
Picture: 13/09/24_Overlap PCR PCR SCPR5_SPCR2 - PCR didn't work


PCR Purification (M13 (EcoRI, PstI), SPCR2 (EcoRI, PstI), SPCR5 (XbaI, SpeI))
Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 50 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

PCR (SPCR2, SPCR3, SPCR5, SPCR6, SPCR7, SPCR8, SPCR9, SPCR10, SPCR11, linearize pSB1C3)
each 8x

Reagent Volume
1x
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 0.5 µl
Reverse Primer (10 uM) 0.5 µl
Template Plasmid 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl




Thermocycler Protocol: Fermentas Phusion
Temp Time
Start 98°C 30 sec Melt
Cycle 1 98°C 5 sec Melt 35 cycles
Cycle 2 25 sec Anneal
Cycle 3 72°C 30 sec per kb Extend
Finish 72 °C 5 min Extand
Store 10°C Forever Store


Liquid culture
NEB, sSP004, Fr-433

Detect

Wednesday 25th September

Gel of PCR, PCR (SPCR5,6) and Miniprep Cas9, M13mp18

Gel of PCR
1%, 100V, 1h

Picture: 13/09/25_SPCR2-11 - SPCR2: worked, SPCR3: worked, SPCR5: didn't work, SPCR6: didn't work, SPCR7: didn't work, SPCR8: didn't work, SPCR9: didn't work, SPCR10: didn't work, SCPR11: worked


PCR (SPCR5,6)

Reagent Volume
x1
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 1 µl
Reverse Primer (10 uM) 1 µl
Template Plasmid) 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl


Thermocycler Protocol: Fermentas Phusion
Temp Time
Start 98°C 30 sec Melt
Cycle 1 98°C 5 sec Melt 35 cycles
Cycle 2 25 sec Anneal
Cycle 3 72°C 30 sec per kb Extend
Finish 72 °C 5 min Extand
Store 10°C Forever Store


Miniprep Cas9, M13mp18
1) Pellet liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension olution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

Detect

Thursday 26th September

Gel PCR 5,6, Digestion, PCR (SPCR7-10) and PCR purification

Gel PCR 5,6 1%, 100V, 1h

Picture: 13/09/26_SPCR5_6 - PCR didn't work


Digestions: SPCR2 (EcoRI, PstI), SPCR3 (EcoRI, PstI), SPCR4 (EcoRI, PstI), SPCR11 (EcoRI, PstI), lin pSB1C3 (EcoRI, PstI), lin pSB1A3 (EcoRI, PstI), SPCR5 (XbaI, SpeI), SPCR7 (XbaI, SpeI), lin pSB1C3 (XbaI, SpeI), in pSB1A3 (XbaI, SpeI)

Reagent Volume
Purified PCR Product 16 µl
H2O 0 µl
10x FastDigest Buffer 2 µl
FastDigest Enzyme 1 1 µl
FastDigest Enzyme 2 1 µl
Total Volume 20 µl


PCR (SPCR7-10)

Reagent Volume
x1
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 1 µl
Reverse Primer (10 uM) 1 µl
Template Plasmid) 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl


Thermocycler Protocol: Fermentas Phusion
Temp Time
Start 98°C 30 sec Melt
Cycle 1 98°C 5 sec Melt 35 cycles
Cycle 2 25 sec Anneal
Cycle 3 72°C 30 sec per kb Extend
Finish 72 °C 5 min Extand
Store 10°C Forever Store



PCR Purification: (SPCR2 (EcoRI, PstI), SPCR3 (EcoRI, PstI), SPCR4 (EcoRI, PstI), SPCR11 (EcoRI, PstI), lin pSB1C3 (EcoRI, PstI), lin pSB1A3 (EcoRI, PstI), SPCR5 (XbaI, SpeI), SPCR7 (XbaI, SpeI), lin pSB1C3 (XbaI, SpeI), in pSB1A3 (XbaI, SpeI)

Add 5 volumes of Buffer PB to 1 volume of the PCR sample and mix.
To bind DNA, apply the sample to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through. Place the QIAquick column back into the same tube
To wash, add 0.75 ml Buffer PE to the QIAquick column and centrifuge for 30–60 s.
Discard flow-through and place the QIAquick column back in the same tube.
Centrifuge the column for an additional 1 min.
Place QIAquick column in a clean 1.5 ml microcentrifuge tube.
To elute DNA, add 50 μl Buffer EB to the center of the QIAquick membrane and centrifuge the column for 1 min.

Detect

Friday 27th September

Gel SPCR7-10, NEB liquid culture, Ligation, Electrocompetent cells and transformation

Gel SPCR7-10
1%, 100V, 1h

Picture: 13/09/27_SPCR7_8_9_10 - PCRs worked


NEB liquid culture
1:1000 of ON culture

Ligation

pS006
Reagent Volume
SPCR5 1 µl
SPCR7 0,28 µl
H2O 7.22 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS006’
Reagent Volume
SPCR5 1 µl
lin pSB1C3 (XbaI/SpeI) 0,47 µl
H2O 7.03 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS006*
Reagent Volume
SPCR5 1 µl
lin pSB1A3 (XbaI/SpeI) 0,67 µl
H2O 6.83 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS013
Reagent Volume
SPCR4 1 µl
SPCR11 0,24 µl
H2O 7.26 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS013'
Reagent Volume
lin pSB1C3 (EcoRI, SpeI) 1 µl
SPCR11 0,28 µl
H2O 7.22 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS013*
Reagent Volume
lin pSB1A3 (EcoRI, PstI)) 1 µl
SPCR11 0,3 µl
H2O 7.2 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS004
Reagent Volume
SPCR4 1 µl
SPCR3 0,2 µl
H2O 7.3 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS004'
Reagent Volume
lin pSB1C3 (EcoRI, PstI) 1 µl
SPCR3 0,3 µl
H2O 7.2 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS004*
Reagent Volume
lin pSB1A3 (EcoRI, PstI) 1 µl
SPCR3 0,27 µl
H2O 7.23 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS002'
Reagent Volume
SPCR2 1 µl
lin pSB1C3 (EcoRI, PstI) 0,8 µl
H2O 6.7 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


pS002*
Reagent Volume
SPCR2 1 µl
lin pSB1A3 (EcoRI, PstI) 0,6 µl
H2O 6.9 µl
Fermentas T4 Ligase Buffer 1 µl
Fermentas T4 Ligase Enzime 0.5 µl
Total Volume 10 µl


45min at 22°, 15 min at 16°

Electrocompetent cells
1) Start Culture
2) When the cells reach an OD600 of 0.2.
3) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
Centrifuge at 4 °C for 10 min at 4000 rpm.
4) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 25 ml of ice cold water
5) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
6) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.

Transformation
pS006, pS006’, pS006*, pS013, pS013’, pS013*, pS004, pS004’, pS004*, pS002’, pS002*

1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)

2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.

3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.

4) Preload a pipette with 1 ml of LB.

5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.

6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.

7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.

8) Incubate 1/2 h at 37 °C with shaking.

9) Plate 10/200 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.

10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.

Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.

Detect

Saturday 28th September

Extraction of Genomic DNA, PCR Reaction and Restreak plates

Protocol: E. coli Colony PCR (pS006’, pS006*, pS013, pS004, pS004*, pS002*)

Extraction of Genomic DNA

1) Pick a single colony into 50 ul of H20.
Fresh colonies (grown that day) work best, but they can also come from 4 C.
Pipet 2ul onto plates to have C1-C8
Pipet 2 ul into 5ml Media with antibiotics to make liquid cultures

2) Boil for 5 minutes.
1.5 ul of this can be used directly for PCR.
Best if used directly, but can also be stored at 4 C for a few days.

PCR Reaction

Keep all the reagents at 4 °C while preparing the mixture.
Pre-heat the thermocycler to 95 °C and transfer your reaction directly from 4 °C.

Reagent Volume 9x Volume
Forward Primer (10 uM) 0.5 µl 4.5 µl
Reverse Primer (10 uM) 0.5 µl 4.5 µl
Template DNA (from above) 1.5 µl 13.5 µl
Quick-Load® Taq 2X Master Mix 12.5 µl 112.5 µl9x Volume
Nuclease-free water 10 µl 90 µl
Total Volume 25 µl 125 µl


Thermocycler Protocol: Green Dream Taq
Temp Time
Start 95°C 30 sec Melt
Cycle 1 95°C 15 sec Melt 35 cycles
Cycle 2 46.8°C 30 sec Anneal
Cycle 3 72°C 1 min per kb Extend
Finish 72 °C 10 min Extand
Store 10°C Forever Store


Restreak plates
Some of the plates were too full grown -> Rstreak for single colonies

Detect

Monday 30th September

Extraction of Genomic DNA, PCR reaction, Gels, Miniprep, PCR: SPCR5, SPCR6 and Liquid culture of pS004’ and pS013’

Protocol: E. coli Colony PCR (pS006, pS013’,pS013*, pS004’, pS002’)

Extraction of Genomic DNA

1) Pick a single colony into 50 ul of H20.
Fresh colonies (grown that day) work best, but they can also come from 4 C.
Pipet 2ul onto plates to have C1-C8

2) Boil for 5 minutes.
1.5 ul of this can be used directly for PCR.
Best if used directly, but can also be stored at 4 C for a few days.

PCR Reaction

Keep all the reagents at 4 °C while preparing the mixture.
Pre-heat the thermocycler to 95 °C and transfer your reaction directly from 4 °C.

Reagent Volume 9x Volume
Forward Primer (10 uM) 0.5 µl 4.5 µl
Reverse Primer (10 uM) 0.5 µl 4.5 µl
Template DNA (from above) 1.5 µl 13.5 µl
Quick-Load® Taq 2X Master Mix 12.5 µl 112.5 µl9x Volume
Nuclease-free water 10 µl 90 µl
Total Volume 25 µl 125 µl


Thermocycler Protocol: Green Dream Taq
Temp Time
Start 95°C 30 sec Melt
Cycle 1 95°C 15 sec Melt 35 cycles
Cycle 2 46.8°C 30 sec Anneal
Cycle 3 72°C 1 min per kb Extend
Finish 72 °C 10 min Extand
Store 10°C Forever Store


Gels
1%, 100V, 45 min

Pictures + Results
13/09/30_colony pcr_pS004_pS013 - 1-8: pS004 (gRNA - Amp), 9-16: pS013 (crRNA - Amp) - seems to have worked beside pS013 C7


13/09/30_colony PCR_pS004*_pS002* - 1-8: pS004* (gRNA - Amp), 9-16: pS002 (reporter - Amp) - pS004* seems to have worked (C1, C2, C3, C6)


13/09/30_colony PCR_pS006'_pS006* - 1-8: pS006' (Cas9 - Chl), 9-16: pS006* (Cas9 - Amp) - didn’t work


13/09/30_Colony PCR_pS013'_pS013* - 1-8: pS013' (crRNA - Chl), 9-16: pS013* (crRNA - Amp) - Seems to have worked beside 13’ C7, C8


13/09/30_colony PCR_pS004'_pS002' - 1-8: pS004' (gRNA - Chl), 9-16: pS002' (reporter - Chl) - pS004' seems to have worked beside C6


13/09/30_Colony PCR_pS006 - didn’t work


other gel images that proof that the reporter as well as the Cas9 construct worked will follow soon!

Miniprep
pS013, pS004
1) Pellet liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension olution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

PCR: SPCR5, SPCR6 (gradient + touch down 55-75, -1°/cycle)

Reagent Volume
11x
Nuclease-free water 37.25 µl
5x Phusion HF Buffer 10 µl
10 mM dNTPs 1 µl
Forward Primer (10 uM) 0.5 µl
Reverse Primer (10 uM) 0.5 µl
Template Plasmid) 0.25 µl
Phusion DNA Polymerase 0.5 µl
Total Volume 50 µl


Thermocycler Protocol: Fermentas Phusion
Temp Time
Start 98°C 30 sec Melt
Cycle 1 98°C 5 sec Melt 35 cycles
Cycle 2 25 sec Anneal
Cycle 3 72°C 30 sec per kb Extend
Finish 72 °C 5 min Extand
Store 10°C Forever Store


Liquid culture of pS004’ and pS013’

Detect

Tuesday 1st October

Miniprep pS013’, pS004’

1) Pellet liquid culture (4000rpm, 10 min)
2) Discard supernatant
3) resuspend the cells in 250ul of resuspension olution
4) add 250ul of lysis solution, mix by inverting 4-6 times
5) add 350ul of neutralization solution
4) centrifuge for 5 min
5) transfer supernatant to spin column
6) centrifuge for 1 min
7) discard flow through
8) add 500 ul wash solution and centrifuge for 1 min , discard flow through(repeat this step)
9) centrifuge for 1 min to remove left over liquid
10) transfer the column on a 1.5ml tube
11) add 50ul of elution buffer and incubate for 2 min
12) centrifuge for 2 min
13) Nanodrop the concentration and freeze at -20°

Detect

Wednesday 2nd October

Preparation killing assay


Liquid cultures
R16, R26, R26f, delta PyrF, parental delta PyrF, NEB, M13, Litmus + Helper, Litmus GFP + helper

Detect

Wedsnesday 3rd October

Killing assay to test specifity of CRISPR Cas

Electrocompetent cells (delta PyrF, parental, NEB)
1) Start Culture
2) When the cells reach an OD600 of 0.2.
3) Harvest the cells.
When the cells reach an OD600 of between 0.6 and 0.8 (OD: 0,683)
Centrifuge at 4 °C for 10 min at 4000 rpm.
4) Wash and combine the cells.
Remove the supernatant.
Resuspend the cells in 25 ml of ice cold water
5) Wash the cells 2 more times.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 50 ml of ice cold water.
Repeat.
6) Wash and concentrate the cells for electroporation.
Centrifuge at 4 °C for 10 min at 4000 rpm.
Resuspend in 1-2 ml of ice cold water.
We will use 200 ul of washed cells per transformation.

Transformation
Cotransform into parental/keio delta pyRF: pS006* (Cas9 in Amp BB) + pS004'(gRNA in Chl BB).
1) Prepare BD tubes with a pipette filled with LB at the interior of each tube (pipette supplied with the electroporation cuvette)
2) Test the purity of the electrocompetent cells.
Add 200 ul of washed cells to a cuvette.
3) Mix the cells and DNA in a cuvette.
200 ul of washed cells with 200 ng of PCR product.
Keep the cuvette on ice until just before the electroporation.
4) Preload a pipette with 1 ml of LB.
5) Pulse the cuvette with voltage.
Dry the electrodes with a kimwipe prior to loading.
Use the EC2 setting.
6) Listen for arcing.
A cracking sound means all the cells are dead.
Note the time constant: 5 is good, 5.8 is great.
7) Immediately recover the cells.
Add the 1 ml of preloaded LB and pipet up and down to mix.
Collect 1 ml of cells, some volume is lost in the cuvette.
8) Incubate 1/2 h at 37 °C with shaking.
9) Plate 10/200 ul of recovered cells on selective plates.
Use antibiotic appropriate to the part being integrated.
Let the other 900 ul rest overnight at room temperature.
10) Concentrate and plate the remaining cells
Spin down quickly and resuspend in 100 ul LB before plating.
Transformed cells should be incubated at 37 °C.
Colonies should appear 24-48 h after plating.


Plating of 10/100ul on
1. Amp plates -> selection for only Cas9
2. Chl plates -> selection for only gRNA
3. Amp/Chl plates -> selection for theoretically functional system

Detect

Monday 14th October

Liquid cultures sSP008, sSP009, R16, R26, R26f, sT007, sSP021, SCPR2-A3, SPCE2-C3

Detect

Tuesday 15th October

Digestion Reporter and SPCR3

BB: SpeI, PstI
SPCR: XbaI, PstI
2h 37°, heat inactivation

Electrocompetent cells: sSP008, sSP009
Transform SPCR2-A3/C3 both into sSP008/9

Detect

Wednesday 16th October

Miniprep of pS002, pS002’, pS006* Liquid culture sSP017, pS004, pS004’ Glycerols

Detect

Thursday 17th October

Place your twit here

Miniprep sSP017, pS004, pS004’

Digest Litmus pS018 EcoRI/PstI, EcoRI/XbaI 2h 37° shaking

PCR purify

Ligation:
1. gRNA+phagmid (10,4+6)
2.phagemid+gRNA+reporter (9,6+1,86+2)
3.phagemid+gRNA+Cas9 (10,2+2,04+3)

1h at 22°

Transform
Heat shock, cells matt
Recover, plate

Detect

Friday 18th October

Miller assay and Liquid phagemid

Place your note here

Detect

Saturday 19th October


Miller
Miniprerp phagemid
Digest phagemid E/P, E/X, SPCR3 E,P

Detect

Tuesday 22nd October

Liquid for Miller and Digest&purify SPCR3 E,P

Detect

Thursday 24th October


Digest phagemid E/P
Purify it

Ligation:
1. SPCR3 E/P + phagemid E/P
2. SPCR3 E/P + SPCR5 P/X+ phagemid E/X
2. SPCR3 E/P + SPCR2 P/X+ phagemid E/X

trafo Ligations

electrocmpetent cells parental+sSP009+pS002’
trafo:
1. parental+pS002
2. parental+pS002’
3. parental+pS006*
4. parental+pS002’+pS006*
5. sSP009 pS002’ + pS006*

trafo helper into NEB

liquid cultures: sSP009, pRECA strains Ariel, sSP008+pS002, sSP008+pS002’

Detect

Friday 25th October


Colony PCR
Liquid Cloning

Liquid: NEB helper, parental pS002, parental pS006*, sSP008+pS002, sSP008+pS002’

Trafo: NEB helper+phageid-gRNA, parental ps006*+pS002’, pyrfF F+ pS002’+pS006*

conjugation of parental pS006* with pS009

Miniprep phagemid gRNA

Liquid library
Restreak for library


1) sSP008+pS002/pS002’ +Xgal
2) sSP008+pS002/pS002’ +Xgal + MMC
3) sSP008+pS002/pS002’ +MMC

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Faculty of Medicine Cochin Port-Royal, South wing, 2nd floor
Paris Descartes University
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75014 Paris, France
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team2013@igem-paris.org
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