Laboratory Notebook
15-06-01
- plate pCas containing NEB10β (#YPKO#) on LB+K and grow at 30 °C
15-06-02
- make steril-filtered arabinose (10 ml, 1 mol/l)
- make chloramphenicol (10 ml)
15-06-03
- make electrocompetent cells with pCas
- 500 µl arabinose added at OD 0.27 (to final concentration of 10 mM)
- calculation of cell density [http://www.genomics.agilent.com/biocalculators/calcODBacterial.jsp?_requestid=14961 Calculator]
15-06-08
- test electrocompetent cells with pUC19 (amp resistance)
- transformed and incubated
15-06-09
- designed and ordered primers #T9T9#, #CT4E#, #6V6P#, #WAO8# and new #A9W9# and #XE3D# from IDT
- transformation of glgX (#1DEN#) and glgP (#C1QW#, #DC6X#, #HCTL#, #4MCW#, pUC19 control) into electrocompetent pCas carrying cells
- plating at 30 °C on LB+K+A plates
15-06-10
- analysis of sequencing results
- overnights in 2 ml LB+K of anti glgX and anti glgP with 10 µl of 100 mM IPTG (0.5 mM final concentration)
- master plates without IPTG on LB+K
15-06-11
- dilution plating of glgX and glgP knockout candidates on LB+K
- plate controls: pCas carrying cells (#YPKO#, LB+K), uncured clones from the trafo plates (antiX/P on LB+K+A)
- analysis of anti glgP sequencings: N20 is intact and the sequences look good
15-06-12
- colony PCR using #A9W9# and #XE3D# to verify plasmid curing
- overnight cultures of good looking clones
- overnights from #YPKO# to get enough sequencing template
15-06-13
- make cryos of glgX and glgP knockout candidates
| construct & clone |
cryo ID |
genomic DNA ID |
PCR product |
purified PCR product |
sequencing result
|
| glgX knockout candidate #2 |
#PH3R# |
#OM6C# |
#LA33#, purified 11+12 |
#FP1F# |
point mutation in the multi stop, but the gene is disrupted
|
| glgX knockout candidate #4 |
#SKKT# |
#1WKE# |
purified |
#1Y4Z# |
-
|
| glgX knockout candidate #5 |
#F93Y# |
#1DOS# |
purified |
#CLR4# |
-
|
| glgP knockout candidate from #HCTL# #1 |
#6RPW# |
#VZD3# |
bad |
- |
-
|
| glgP knockout candidate from #HCTL# #3 |
#XC4Y# |
#TWZ1# |
- |
- |
-
|
| glgP knockout candidate from #HCTL# #4 |
#CKT3# |
#MMLP# |
- |
- |
-
|
| glgP knockout candidate from #HCTL# #5 |
#NN38# |
#NKOA# |
- |
- |
-
|
| glgP knockout candidate from #4MCW# #2 |
#1SHE# |
#1RM3# |
#LOFF#:P1 |
#NP3B# |
no chromatograms
|
| glgP knockout candidate from #4MCW# #3 |
#TSBH# |
#O1FO# |
- |
- |
-
|
| glgP knockout candidate from #4MCW# #4 |
#BH9D# |
#E3E9# |
- |
- |
-
|
| glgP knockout candidate from #4MCW# #5 |
#HHTX# |
#1QAT# |
- |
- |
-
|
| glgP knockout candidate from #C1QW# #2 |
#BWXX# |
#FFA9# |
#LOFF#:P2 |
#PY96# |
no chromatograms
|
| glgP knockout candidate from #C1QW# #3 |
#Z1E3# |
#CAAV# |
- |
- |
-
|
| glgP knockout candidate from #C1QW# #4 |
#RS8L# |
#SRKE# |
- |
- |
-
|
| glgP knockout candidate from #C1QW# #5 |
#FQ6W# |
#A6OB# |
- |
- |
-
|
- extraction of genomic DNA
- plasmid prep pCas from the frozen overnights (#APMK#, #63ZY#)
15-06-15
- measure extracted DNA concentrations
- dilute genomic DNA to 500 ng/µl
- PCR-amplify the genomic regions of glgX and glgP knockouts with 1000 ng/50 µl reaction
- glgX #OM6C# with #6V6P# and #WAO8# 55-64 °C (expected: 1024, maybe: 1006) > products in #LA33#, 63.5 is the best annealing temperature
- glgP #VZD3# with #T9T9# and #CT4E# 55-64 °C (expected: 1015, maybe: 3351) > products in #DOMW#
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
98 |
0'30"
|
| denaturation |
98 |
0'30"
|
| gradient annealing |
55-64 |
0'30"
|
| elongation |
72 |
0'33" (glgX) or 1'43" (glgP)
|
| final elongation |
72 |
5'00"
|
- amplify the genomic regions of all remaining candidates
- annealing temperature for glgX 63.5 °C
- annealing temperature for glgP 63.9 °C (product from #1RM3# is #LOFF#:P1 and from #FFA9# is #LOFF#:P2)
- PCR product purification
- pipette purified PCR products for sequencing
- pipette pCas plasmids for sequencing with 5 of 32 primers, because we don't have enough template DNA...
15-06-16
- PCR product purification of P1 and P2 from #LOFF#
- agarose gel of 2.5 µl P1/P2 and 0.5 µl loading dye (the gel is wrapped in foil in our 4° fridge) -> no visible bands except ladder
- sequencing of genomic glgX and glgP regions
- bring the sequencing samples to the Fraunhofer IME because you are too late ;-)
- colony PCR on glgP (from plate of #C1QW# and cured) and glgX (from plate #1DEN# and cured) knockout candidates
| parameter |
glgP |
glgX genomic (1024 bp) |
glgX edit (531 bp)
|
| forward primer |
#T9T9# |
#6V6P# |
#SNYO#
|
| reverse primer |
#CT4E# |
#WAO8# |
#WAO8#
|
| denaturation |
0'15" |
0'15" |
0'15"
|
| annealing [°C] |
62.0 |
63.5 |
63.5
|
| annealing time |
0'15" |
0'15" |
0'15"
|
| elongation time |
1'43" |
0'33" |
0'33"
|
| picking instructions
|
colony > PCR tube > master plate
|
colony > 5 µl water > (master plate, 1 µl into PCR tube)
|
15-06-17
- electroporation of anti glgP plasmid into 25 µl electrocompetent pCas cells
- arabinose added to every 500 µl of SOC medium (to final concentration of 10 mM)
- 2 µl of plasmid DNA (#C1QW#, #HCTL#, #4MCW#)
- colony PCR of negative control (cryo #YPKO#) for glgX genomic PCR with #SNYO# and #WAO8#
| time |
temperature
|
| 10:00 |
94°C
|
| 00:15 |
94°C
|
| 00:15 |
58°C
|
| 00:33 |
68°C
|
| 02:00 |
68°C
|
- sequencing results: #PH3R# is an almost perfect knockout of glgX
15-06-18
- colony PCR on many glgP colonies (controls!)
- resuspended the cells in 5 µl LB+K
- primers #T9T9# and #CT4E#
- 1-11: knockout candidate from #C1QW#
- 13-23: knockout candidates from #HCTK#
- 24-35: knockout candidates from #4MCW#
- master plate in parallel with 400 µl IPTG
- overnight cultures (2ml) of good looking colonies with 40 µl IPTG
15-06-19
Cryos and genomic DNA extraction of the glgP knockout candidates
| candidate |
cryo ID |
genomic DNA |
PfuS PCR product |
purified ID |
sequencing result
|
| from #C1QW# clone #7 |
#DK14# |
#FQEL# |
#YWMH#:P7 |
#YOCW# |
bad sequencing
|
| from #C1QW# clone #9 |
#XHEK# |
#QQFH# |
#YWMH#:P9 |
#KFX4# |
probably perfect (selected)
|
| from #C1QW# clone #10 |
#FEHT# |
#CS83# |
#YWMH#:P10 |
#4ZXT# |
probably perfect
|
PfuS PCR to amplify the genomic region. The products are in #YWMH#.
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #T9T9# and #CT4E# |
62 |
0'30"
|
| elongation |
72 |
1'43"
|
| final elongation |
72 |
5'00"
|
15-06-22
- heat shock transformation of 4 µl pCas (#EANB#) into 100 µl BL21 Gold (DE3) from the Schwaneberg group (plated on LB+K at 30 °C)
- PCR product purifications from #YWMH# (see table above)
- pipetted purified PCR products for sequencing with #T9T9#, #CT4E# and #WQRS#
15-06-23
- plate glgP knockout candidates #DK14#, #XHEK# and #FEHT# on LB+K+IPTG and grow at 30 °C (preparation for competent cells on Thursday)
- master plate of pCas in BL21(DE3) and grow at 30 °C
- make an overnight culture of a pCas in BL21(DE3) clone and grow at 30 °C
- aliquot buffers into numbered falcons (like we did the first time)
15-06-24
- cryo of pCas in BL21 Gold (DE3) -> #RMBC#
- analyze sequencing results
- from masterplates make overnight precultures (LB+K) of pCas in BL21(DE3) and one good glgP knockout strain (sequencing #KFX4#, corresponding cryo #XHEK#)
15-06-25
- make electrocompetent cells (see manual: genome editing)
- inoculated main culture at 10:00
- arabinose 500 µL in 50 mL
- pCas in NEB10β-ΔglgP (induced at OD=0.27)
- pCas in BL21(DE3) (induced at OD=0.38)
- at 13:20 pCas= OD 0.781 anti glgP= OD 0.512: cool down!
- measure OD before aliquoting: NEB10β-ΔglgP: OD=20 BL21(DE3): OD=28.2
- aliquot 25 µl into PCR tubes and freeze them in big falcons!
15-06-26
15-06-29
Transformations to be plated on LB+K+A
| strain |
transformed with |
result
|
| NEB10β-ΔglgP-pCas-cells |
nothing |
no colonies
|
| NEB10β-ΔglgP-pCas-cells |
#1DEN# |
small colonies
|
| BL21 Gold (DE3)-pCas |
#C1QW# |
no colonies
|
15-06-30
- colony PCR on glgPX knockout candidates (5 µl LB+K in PCR tube, master plate LB+K of 1, 3, 4, 5, 6, 7, 8, 9, overnights+IPTG of clones 3, 4, 5, 7)
| template |
tube |
forward primer |
reverse primer |
purpose |
expected length
|
| NEB10β-ΔglgP glgX knockout candidate 1-12 |
1-12 |
#SNYO# |
#WAO8# |
find edited clones |
531 bp
|
| NEB10β-ΔglgP glgX knockout candidate 13 |
13 |
#SNYO# |
#K4TH# |
to confirm that #SNYO# binds on the plasmid |
463 bp
|
| NEB10β-ΔglgP |
14 |
#SNYO# |
#WAO8# |
negative control |
no bands
|
| NEB10β-ΔglgP |
15 |
#6V6P# |
#WAO8# |
to see if the PCR worked |
1024 bp
|
| picking instructions for 1-13
|
colony > 5µl LB+K > (master plate, 1 µl into PCR tube)
|
| elongation time
|
1'10"
|
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
94 |
10'00"
|
| denaturation |
94 |
0'30"
|
| annealing |
63.5 |
0'30"
|
| elongation |
72 |
1'10"
|
| final elongation |
72 |
5'00"
|
- overnight cultures of good knockout candidates
Electroporations
| strain |
plasmid |
purpose
|
| BL21 Gold (DE3)-pCas |
#LYZH# |
testing the electrocompetence
|
| BL21 Gold (DE3)-pCas |
#C1QW# |
glgP knockout
|
15-07-01
- cryo + genomic DNA extraction
| clone |
cryo ID |
genomic DNA ID |
purified PfuS PCR product |
sequencing result
|
| NEB10β ΔglgP ΔglgX candidate #3 |
#WVKQ# |
#HMYH# |
#AT9O# |
perfect glgX knockout
|
| NEB10β ΔglgP ΔglgX candidate #4 |
#LNL4# |
#L4P1# |
#MMCH# |
perfect glgX knockout
|
| NEB10β ΔglgP ΔglgX candidate #5 |
#39Y9# |
#DHOL# |
#DMNT# PCR did not work |
-
|
| NEB10β ΔglgP ΔglgX candidate #7 |
#ELM1# |
#WWTY# |
#APMY# PCR did not work |
-
|
PfuS PCR to amplify the genomic region. The products are in #SHYS#.
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'33" (1024 bp)
|
| final elongation |
72 |
2'00"
|
| reaction volume |
50 µl |
|
| template DNA |
2 µl per reaction |
|
- PCR product purification
- pipette for sequencing
- colony PCR to check for pSB1A3 curing
- overnight of pSB1A30 in BL21 clones + IPTG (gave them to iSK/iLG/iTS)
- PCR on glgP knockout in BL21
- primers #T9T9# and #CT4E#
- knockout candidate from #C1QW#
- resuspend glgP knockout candidates in 5 µl LB medium
colony PCR on BL21 Gold DE3 glgP knockout candidates
| template |
tube |
forward primer |
reverse primer |
purpose |
expected length
|
| BL21 Gold DE3 glgP knockout candidate 1-24 |
1-24 |
#T9T9# |
#CT4E# |
find edited clones |
1015/3351 bp
|
| NEB10β-ΔglgP |
25 |
#T9T9# |
#CT4E# |
positive control with desired length |
1015 bp
|
| BL21 Gold DE3-pCas-pSB1A30 |
26 |
#T9T9# |
#CT4E# |
negative control with no knockout |
3351 bp
|
| LB+K |
27 |
#T9T9# |
#CT4E# |
negative control |
no bands
|
| picking instructions for 1-13
|
colony > 5µl LB+K > (master plate, 1 µl into PCR tube)
|
| elongation time
|
1'10"
|
30 cycles with KAPA2G Fast Ready Mix
| step |
temperature [°C] |
duration
|
| initial denaturation |
95 |
10'00"
|
| denaturation |
95 |
0'30"
|
| annealing |
62 |
0'30"
|
| elongation |
72 |
0'55" (1015/3351 bp)
|
| final elongation |
72 |
2'00"
|
The colony PCR was not very successful. Many samples did not work, including the controls. Nevertheless, we have identified three candidates (4, 18, 20).
Overnight cultures of good knockout candidates 4, 18, 20. 2 ml of LB+K+IPTG were inoculated with 2 µl of suspended cells
15-07-02
- make cryos and genomic DNA isolations of BL21 Gold DE3 glgP knockout candidates
| clone |
cryo ID |
genomic DNA ID |
purified PfuS PCR product |
sequencing result
|
| BL21 Gold (DE3) ΔglgP candidate #4 |
#3RZ1# |
#8V4S# |
#9KST# |
perfect (selected)
|
| BL21 Gold (DE3) ΔglgP candidate #18 |
#ZTYF# |
#4DTX# |
#YSBT# |
perfect
|
| BL21 Gold (DE3) ΔglgP candidate #20 |
#MEWN# |
#99LV# |
#4BX6# |
perfect
|
PfuS PCR to amplify the genomic region. The products are in #DO3L#.
Positive control: #QQFH# (tube 7)
Negative control: water (tube 8)
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
5'00"
|
| denaturation |
98 |
0'30"
|
| annealing #T9T9# and #CT4E# |
62.0 |
0'30"
|
| elongation |
72 |
1'43" (1015 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA |
2 µl per reaction |
|
15-07-03
- purified yesterdays PfuS PCR products of BL21 glgP knockout candidates
15-07-06
- pipette for sequencing
- plate anti glgX glgP double knockout candidate in NEB10β on LB- +IPTG and incubate first at 30 °C then at 37 °C to cure both plasmids
- plate anti glgP in BL21 Gold (DE3) on LB+K+IPTG and incubate at 30 °C
15-07-07
- plate double knockout candidate in NEB10β on LB+K to test if pCas is cured
- overnights of cured double-knockout candidates for cryo cultures
15-07-08
- overnights of ΔglgP in BL21 for electrocompetent cells
- cryos of cured double-knockout candidates
- test on LB+K+A showed that curing had worked
15-07-08
- analysis of sequencing results
- overnight culture of BL21 Gold (DE3) ΔglgP (from #3RZ1#) on LB+K at 30 °C
15-07-09
- inoculated main culture at 9:20 am
- prepare aliquots of buffers for electrocompetent cells
| time |
OD
|
| 1 |
0.068
|
| 2.33 |
0.245
|
- make electrocompetent BL21 Gold (DE3) ΔglgP cells
- transform by electroshock:
- #LYZH# into BL21 Gold (DE3) ΔglgP for testing electrocompetence
- #1DEN# into BL21 Gold (DE3) pCas for single knockout
- #1DEN# into BL21 Gold (DE3) ΔglgP for double knockout in BL21
15-07-10
- none of the electroporations worked!
- repeat transformations:
- #LYZH# into BL21 Gold (DE3) ΔglgP for testing electrocompetence
- #1DEN# into BL21 Gold (DE3) pCas for single knockout
- #1DEN# into BL21 Gold (DE3) ΔglgP for double knockout in BL21
15-07-11
- put transformation plate in the fridge until Monday
Transformations plated on LB+K+A
| strain |
transformed with |
result
|
| BL21-ΔglgP-pCas-cells |
#LYZH# |
>100 colonies
|
| BL21-pCas-cells |
#1DEN# |
2 colonies
|
| BL21-ΔglgP-pCas-cells |
#1DEN# |
8 colonies
|
15-07-13
- parallel masterplates and overnights of good clones
| parameter |
glgX genomic (1024 bp) |
glgX edit (531 bp)
|
| forward primer |
#6V6P# |
#SNYO#
|
| reverse primer |
#WAO8# |
#WAO8#
|
| picking instructions
|
colony > 5 µl water > (master plate, 1 µl into PCR tube)
|
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
94 |
10'00"
|
| denaturation |
94 |
0'30"
|
| annealing |
63.5 |
0'30"
|
| elongation |
72 |
1'10"
|
| final elongation |
72 |
5'00"
|
15-07-14
- gel shows that all glgX double-knockouts in BL21 have worked
- just clone #1 of the single-knouckout in BL21 looks good
- cryos
- genomic DNA extraction
| clone |
genomic DNA stored in
|
| glgX #1 |
#AABE#
|
| glgXP #1 |
#9NMT#
|
| glgXP #2 |
#XRQA#
|
| glgXP #3 |
#XBRK#
|
- PfuS PCR to amplify the genomic region. The products are in #9SBX#.
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
5'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'35" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA |
2 µl per reaction |
|
- tube 1: glgX single-knockout BL21 #1
- tube 2: glgXP double-knockout BL21 #1
- tube 3: glgXP double-knockout BL21 #2
- tube 4: glgXP double-knockout BL21 #3
- tube 5: water control
- PfuS PCR did not work!!! will be repeated
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'35" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA |
2 µl per reaction |
|
products stored in #9SBX#
15-07-15
- Check PCR products on gel: all samples have correct length
- PCR product purification
| clone |
cryo ID |
genomic DNA ID |
purified PfuS PCR product |
sequencing result
|
| BL21 Gold (DE3) ΔglgX candidate #1 |
#ZPKP# |
#AABE# |
#M6DH# |
perfect
|
| BL21 Gold (DE3) ΔglgP ΔglgX candidate #1 |
#CK4H# |
#9NMT# |
#E8PP# |
negative
|
| BL21 Gold (DE3) ΔglgP ΔglgX candidate #2 |
#A3Y6# |
#XRQA# |
#COYB# |
negative
|
| BL21 Gold (DE3) ΔglgP ΔglgX candidate #3 |
#LMNN# |
#XBRK# |
#3DNC# |
negative
|
15-07-17
- electroporation of #1DEN# into BL21 Gold (DE3) cells with pCas
- IPTG (30 °C) and pCas curing (37°C) of #3RZ1#, #ZPKP#, #PH3R# and #XHEK#
- overnight culture of BL21 Gold DE3
15-07-18
- OneTaq PCR on edited genome:
- 4 clones, #3RZ1# as negative control, #ZPKP# as positive control
- no bands for #1, clones #3 and #4 look best
| parameter |
glgX genomic (1024 bp) |
glgX edit (531 bp)
|
| forward primer |
#6V6P# |
#SNYO#
|
| reverse primer |
#WAO8# |
#WAO8#
|
| picking instructions
|
colony > 5 µl water > (master plate, 1 µl into PCR tube)
|
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
94 |
10'00"
|
| denaturation |
94 |
0'30"
|
| annealing |
63.5 |
0'30"
|
| elongation |
68 |
1'10"
|
| final elongation |
68 |
5'00"
|
pipetting table (to be done for each master mix)
| component |
amount [µl]
|
| H20 |
48
|
| #WAO8# (#WAO8#) |
6
|
| #6V6P# (#SNYO#) |
6
|
| 2xMM OneTaq |
75
|
- overnight cultures with IPTG of good clones
- plate cured #3RZ1#, #ZPKP#, #PH3R# and #XHEK# on LB+K and LB+A (control) and make an LB- overnight
- cryo of BL21 Gold DE3
15-07-19
- Curing did not work 100%, so we re-plated the knockout strains on a new LB- plate
Cryo cultures and genomic DNA preparation of glgXP double knockout candidates
| strain |
cryo |
genomic DNA |
purified PCR product |
sequencing result
|
| BL21 Gold DE3 glgXP candidate #1 |
#H49M# |
#LW4W# |
- |
|
| BL21 Gold DE3 glgXP candidate #2 |
#VENK# |
#4ORE# |
#CXQY# |
did not work
|
| BL21 Gold DE3 glgXP candidate #3 |
#KENF# |
#SW4F# |
#OSW1# |
did not work
|
| BL21 Gold DE3 glgXP candidate #4 |
#D8XW# |
#KHRV# |
#S9NT# |
did not work
|
15-07-20
- plated cells to cure from LB- on LB+K and on LB+A again
- measure and dilute genomic DNA (table above)
- PfuS PCR to amplify genomic region of glgX knockout
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'35" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA |
2 µl per reaction |
|
products in #PVFC#
- gel of PCR products: clones #2-4 look good and are purified (see table above)
15-07-21
- curing did not work again!
- to test the LB+K plate, we plated:
| template |
ID |
expectation |
result
|
| sfGFP in pSB1A3 |
#IBF4# |
no growth |
strong growth
|
| glgXP double knockout NEB10β |
#WHPX# |
no growth |
no growth
|
| NEB10β |
#ZEYD# |
no growth |
no growth
|
| BL21 Gold (DE3) |
#34CT# |
no growth |
no growth
|
| BL21 Gold (DE3) ΔglgP |
cryo: #3RZ1# |
no growth |
growth
|
15-07-22
- we did not pick single colonies from LB- plate, so we repeat curing
- three single colonies from each LB- plate (#3RZ1#, #ZPKP#, #PH3R# and #XHEK#) are picked and streaked on LB- and LB+K
- none of the BL21 glgXP double knockouts worked!
| strain |
cryo |
genomic DNA |
purified PCR product |
sequencing result
|
| BL21 Gold DE3 glgXP candidate #1 |
#H49M# |
#LW4W# |
- |
|
| BL21 Gold DE3 glgXP candidate #2 |
#VENK# |
#4ORE# |
#CXQY# |
did not work
|
| BL21 Gold DE3 glgXP candidate #3 |
#KENF# |
#SW4F# |
#OSW1# |
did not work
|
| BL21 Gold DE3 glgXP candidate #4 |
#D8XW# |
#KHRV# |
#S9NT# |
did not work
|
15-07-23
- Curing:
- #ZPKP# -> all three clones were cured
- #XHEK# -> only the first clone was cured
- #3RZ1# and #PH3R#-> curing did not work for any clone
- make overnights of the cured clones LB-
- for #3RZ1# and #PH3R#: pick 6 more colonies and test them on LB+K (also plate on LB-)
- double knockout did not work again!
- we will test if our electrocompetent BL21 (DE3) ΔglgP still have the pCas by plating them on LB+K (30 °C)
15-07-24
- electrocompetent BL21 ΔglgP still have the pCas
- curing just worked for one clone of #PH3R#
- make overnights of the cured clone #2 from #PH3R# in LB-
- #3RZ1# was not cured: pick more colonies to cure
15-07-25
- cryo culture of cured #PH3R# (ID: #CL6W#)
- put LB+K and LB- of #3RZ1# into fridge
15-07-27
- overnight of cured #3RZ1# clone #8 in LB-
15-07-28
- cryo of cured #3RZ1# clone #8 in #FVNV#
15-07-29
15-07-30
- make overnight from plate
- PfuS PCR to check BL21 knockouts again (NEB10β did not grow on M9)
- for X knockout tubes 3+4:
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'35" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA #VBTL# |
2 µl per reaction |
|
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #T9T9# and #CT4E# |
62 |
0'30"
|
| elongation |
72 |
1'43" (1015 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA #C1BL# |
2 µl per reaction |
|
- products are stored in #WWP8#
15-07-31
- make new sterile filtered arabinose: for 10 ml of 1M solution: 1.5 g arabinose
- make electrocompetent NEB10β-ΔglgX-ΔglgP cells and BL21-ΔglgX cells (see manual: genome editing)
- inoculated main culture at 09:45
- NEB10β-ΔglgP-ΔglgX
- BL21(DE3)-ΔglgX (induced at OD=0.288)
- at 12:10 BL21= OD 0.515: cool down!
- at NEB10β= OD 0.51: cool down!
- measure OD before aliquoting: NEB10β-ΔglgP-ΔglgX: OD=18 BL21(DE3)-ΔglgX: OD=25
- aliquot 25 µl into PCR tubes and freeze them in big falcons!
- repeat PfuS PCR to check BL21 ΔglgX
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'35" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA #VBTL# |
2 µl per reaction |
|
- PfuS did not work! No bands are on the gel
15-08-03
- electroporation of #C1QW# into electrocompetent BL21 ΔglgX
- control: #LYZH#
- make an overnight culture of #XFWX#
15-08-04
- masterplate of Bl21 (DE3) Gold anti-glgX-glgP +IPTG on LB+K
- repeat PfuS PCR to check BL21 ΔglgX from #XFWX#: extracted genomic DNA: #WBKH#
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'38" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA #WBKH# |
2 µl per reaction |
|
- gel looks good
- PCR clean-up
- product in #LRCC#
- #LRCC# was sent into sequencing
15-08-05
- no colonies on masterplate of Bl21 (DE3) Gold anti-glgX-glgP
- make a gel to check if #C1QW# is okay
- repeat transformation of #C1QW# in BL21 anti-glgX electrocompetent cells
- added 5 µl arabinose to SOC medium
- #C1QW# is empty and discarded
15-08-06
- colony PCR on colonies from trafo plate
- double knockout in BL21 did not work again!
15-08-07
- repeat electroporation of newly purified #C1QW# in Bl21 (DE3) Gold ΔglgX
- no colonies visible on the plate!
- repeat electroporation with different voltage
| tube # |
competent cells |
transformed plasmid |
purpose |
result
|
| 1 |
BL21 Gold (DE3) ΔglgX |
#C1QW# |
BL21 double knockout |
no colonies
|
| 2 |
BL21 Gold (DE3) ΔglgX |
#LYZH# |
control |
no colonies
|
| 3 |
BL21 Gold (DE3) with pCas |
#C1QW# |
test #C1QW# (targeting plasmid) |
no colonies
|
| 4 |
BL21 Gold (DE3) with pCas |
#LYZH# |
control |
ok
|
15-08-08
- transformation has not worked again
15-08-10
- electroporation of #1DEN# in BL21 antiX and #C1QW# in antiP electrocompetent
- 10 µl arabinose in SOC medium
- plate and overnight of #C81O# and #FVNV# to make electrocompetent cells
15-08-11
- repeat electroporation because there were just a few colonies
- 10 µl arabinose in SOC medium
- make electrocompetent cells of cured BL21 anti glgX #C81O# and BL21 anti glgP #FVNV#
- accidentally, cells were centrifuged at 1000 rpm, not 1000 g :-(((
- colony Taq PCR on colonies with #1DEN# (no colonies on plate with #C1QW#)
| parameter |
glgX genomic (1024 bp) |
glgX edit (531 bp)
|
| forward primer |
#6V6P# |
#SNYO#
|
| reverse primer |
#WAO8# |
#WAO8#
|
| picking instructions
|
colony > 5 µl water > (master plate, 1 µl into PCR tube)
|
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
94 |
10'00"
|
| denaturation |
94 |
0'30"
|
| annealing |
63.5 |
0'30"
|
| elongation |
68 |
1'10"
|
| final elongation |
68 |
5'00"
|
| no |
template |
primers
|
| 1 |
1DEN no 1 |
WAO8, 6V6P
|
| 2 |
1DEN no 2 |
WAO8, 6V6P
|
| 3 |
1DEN no 3 |
WAO8, 6V6P
|
| 4 |
1DEN no 4 |
WAO8, 6V6P
|
| 5 |
1DEN no 5 |
WAO8, 6V6P
|
| 6 |
AVQR negative control |
WAO8, 6V6P
|
| 8 |
1DEN no 1 |
WAO8, SNYO
|
| 9 |
1DEN no 2 |
WAO8, SNYO
|
| 10 |
1DEN no 3 |
WAO8, SNYO
|
| 11 |
1DEN no 4 |
WAO8, SNYO
|
| 12 |
1DEN no 5 |
WAO8, SNYO
|
| 13 |
AVQR negative control |
WAO8, SNYO
|
| 14 |
water control |
WAO8, SNYO
|
- make a master plate of double knockout candidates (LB+K+IPTG) in parallel
- gel of anti XP knockout candidate Taq PCR
- clone number 1-4 look good
- make overnights (LB+K+IPTG) of good knockout clones
- make overnights of #C81O# and #FVNV# to make new electrocompetent cells
- make an LB+A plate of #BAB3# to make new #1DEN#
15-08-12
- no colonies on plate with #C1QW# in BL21 ΔglgX
- a few colonies on plate with #1DEN# in BL21 ΔglgP
- made a master plate with six clones
- many colonies on plate of #LYZH# (control)
- made electrocompetent cells
- inoculate main culture of #C81O# and #FVNV# at 10:25
- OD of ΔglgX: 21.7
- OD of ΔglgP: 20.1
- made cryo cultures of double knockout candidates and extracted genomic DNA
| clone |
cryo |
extracted genomic DNA
|
| 1 |
#8Y3P# |
#3996#
|
| 2 |
#SVSX# |
#XCQO#
|
| 3 |
#QBVS# |
#ZPDW#
|
| 4 |
#FNWA# |
#WNTA#
|
- PfuS PCR to check BL21 ΔglgXP knockout candidates
30 cycles
| parameter |
value |
duration
|
| initial denaturation |
98 |
10'00"
|
| denaturation |
98 |
0'30"
|
| annealing #6V6P# and #WAO8# |
63.5 |
0'30"
|
| elongation |
72 |
0'38" (1024 bp)
|
| final elongation |
72 |
5'00"
|
| reaction volume |
50 µl |
|
| template DNA |
2 µl per reaction |
|
products stored in #938K#
- no 1 and 2 looked good on the gel
- PCR purification (1: #A6XM#, #C3B3#)
- #BAB3# overnight culture (LB+A)
15-08-13
- pipette #A6XM# and #C3B3# for sequencing
- prep #BAB3# overnight culture for new #1DEN#
- One Taq PCR on new #1DEN# in BL21 ΔglgP
| parameter |
glgX genomic (1024 bp) |
glgX edit (531 bp)
|
| forward primer |
#6V6P# |
#SNYO#
|
| reverse primer |
#WAO8# |
#WAO8#
|
| picking instructions
|
colony > 5 µl water > (master plate, 1 µl into PCR tube)
|
30 cycles
| step |
temperature [°C] |
duration
|
| initial denaturation |
94 |
10'00"
|
| denaturation |
94 |
0'30"
|
| annealing |
63.5 |
0'30"
|
| elongation |
68 |
1'10"
|
| final elongation |
68 |
5'00"
|
- run an agarose gel
- clone 3,4,6 look good on gel
- #SNYO# and #WAO8# also amplify regions of clones without iGEM MultiStop (with and without targeting plasmid)
- make overnight cultures (LB+K+IPTG) of good clones
15-08-14
- cryo cultures of BL21 ΔglgPΔglgX k.o. candidates
| clone |
cryo ID |
purified genomic DNA ID |
tube in PfuS PCR |
purified PCR product |
sequencing result
|
| BL21 ΔglgXΔglgP #3 |
#EVAL# |
#KNOF# |
1+2 |
#ALPF# |
|
| BL21 ΔglgXΔglgP #4 |
#36VR# |
#RBP3# |
3+4 |
#WQ4L# |
|
| BL21 ΔglgXΔglgP #6 |
#YFH1# |
#S8S1# |
5+6 |
#HS4M# |
concentration was too low
|
- genomic DNA extraction
- PfuS PCR on knockout candidates (tube 7: water control)
- gel: tube 1,2,4 and 5 were good
- PCR clean-up
- pipette for sequencing
Results
| strain |
cryo with pCas |
cryo without plasmids (LB) |
cryo without plasmids (M9)
|
| DH5a |
|
#VD49# |
|
| NEB10β |
#YPKO# |
#ZEYD# |
|
| NEB10β ΔglgX (1 mutation in the Multi Stop) |
#PH3R# |
#CL6W# |
|
| NEB10β ΔglgP |
#XHEK# |
#BXR1# |
|
| NEB10β ΔglgX ΔglgP |
#LNL4# |
#WHPX# |
|
| BL21 Gold (DE3) |
#RMBC# |
#34CT# |
#E4B3#
|
| BL21 Gold (DE3) ΔglgX |
#ZPKP# |
#C81O# |
#XFWX# confirmed again by sequencing
|
| BL21 Gold (DE3) ΔglgP |
#3RZ1# |
#FVNV# |
#4BW3#
|
| BL21 Gold (DE3) ΔglgX ΔglgP with pCas |
|
|
|