Team:Fatih-Medical/Lab/Diary

From 2012.igem.org

(Difference between revisions)
Line 66: Line 66:
'''Thursday'''
'''Thursday'''
-
-We made isolation for P2L1,P2L3,H1,C2,L2 and then digestion has been made with EcoR1 and Pst1 for all of these parts.After that electrophoresis was performed for these parts.
+
 
-
-The results of P2L1 and P2L3 might be true , we are not sure about this so we need some expert assistance and we need to sequence these part for being sure. Unfortunately the result of L2 was wrong again.
+
* We made isolation for P2L1,P2L3,H1,C2,L2 and then digestion has been made with EcoR1 and Pst1 for all of these parts.After that electrophoresis was performed for these parts.
-
-We prepared a new liquid culture for L2.
+
* The results of P2L1 and P2L3 might be true , we are not sure about this so we need some expert assistance and we need to sequence these part for being sure. Unfortunately the result of L2 was wrong again.
 +
* We prepared a new liquid culture for L2.
Line 75: Line 76:
'''Friday'''
'''Friday'''
-
-In order of isoation, digestion and electrophoresis was performed to L2 and C2.By the way electrophoresis was performed 2 times for being sure but both of results were wrong.
+
 
-
-Digestion has been made with Xba1 and Spe1 for H1.
+
* In order of isoation, digestion and electrophoresis was performed to L2 and C2.By the way electrophoresis was performed 2 times for being sure but both of results were wrong.
-
-Ligation was performed for P2 and H1 ,C1 and GFP.
+
* Digestion has been made with Xba1 and Spe1 for H1.
 +
* Ligation was performed for P2 and H1 ,C1 and GFP.
Line 84: Line 86:
'''Wednesday'''
'''Wednesday'''
-
- Transformation has been made for C2,L2,P2H1 and C1-GFP (unsuccessful)
+
 
-
- We prepared 200 ml LB broth for next experiments.
+
* Transformation has been made for C2,L2,P2H1 and C1-GFP (unsuccessful)
 +
* We prepared 200 ml LB broth for next experiments.
'''Thursday'''
'''Thursday'''
-
- Transformation has been made for C2,L2,P2H1 and C1-GFP.
+
 
-
-C2 and L2 (successful)
+
* Transformation has been made for C2,L2,P2H1 and C1-GFP.
 +
* C2 and L2 (successful)
'''Friday'''
'''Friday'''
-
- We prepared 200 ml LB broth and 15 plates for next experiments
+
 
-
- Transformation was made for P2H1 and C1-GFP.
+
* We prepared 200 ml LB broth and 15 plates for next experiments
-
- We prepared liqued culture for C2 and L2.
+
* Transformation was made for P2H1 and C1-GFP.
 +
* We prepared liqued culture for C2 and L2.
'''Saturday'''
'''Saturday'''
-
- Single colony isolation has been made for C2 and L2.
+
 
-
-C2 and L2 are digested with EcoR1 and Pst1.
+
* Single colony isolation has been made for C2 and L2.
 +
* C2 and L2 are digested with EcoR1 and Pst1.
Line 105: Line 111:
'''Monday'''
'''Monday'''
-
-electrophoresis was performed for C2 and L2.(Unsuccessful)
+
 
-
-We prepared Tfb1 and Tfb2 for compatent cell.
+
* electrophoresis was performed for C2 and L2.(Unsuccessful)
-
-We prepared liquid culture for C2 and L2.
+
* We prepared Tfb1 and Tfb2 for compatent cell.
 +
* We prepared liquid culture for C2 and L2.
'''Tuesday'''
'''Tuesday'''
-
- Single colony isolation has been made for C2 and L2.
- electrophoresis was performed for C2 and L2.
+
 
-
- C2 and L2 are digested with EcoR1 and Pst1.
+
* Single colony isolation has been made for C2 and L2.
- electrophoresis was performed for C2 and L2.
 +
* C2 and L2 are digested with EcoR1 and Pst1.
Line 118: Line 126:
'''Monday'''
'''Monday'''
-
- We added compotent cells to ampicilin included liquid culture and plate.
+
 
-
-We added compotent cells to cloramphenicoli included plate.
+
* We added compotent cells to ampicilin included liquid culture and plate.
-
-We incubated cloramphenicol resistance bacteria to ampicilin included plate.
+
* We added compotent cells to cloramphenicoli included plate.
-
-We added compatent cells to plate without antibiotic.
+
* We incubated cloramphenicol resistance bacteria to ampicilin included plate.
 +
* We added compatent cells to plate without antibiotic.
'''Tuesday'''
'''Tuesday'''
-
-We prepared 15 CHL plates.
+
 
-
-We tested compatent cell by RFB transformation.
+
* We prepared 15 CHL plates.
-
-We prepared liquid culture for preparetion of compatent cell.
+
* We tested compatent cell by RFB transformation.
 +
* We prepared liquid culture for preparetion of compatent cell.
'''Wednesday'''
'''Wednesday'''
-
- Transformation was made for C2,L2 and C1-GFP.
+
 
 +
* Transformation was made for C2,L2 and C1-GFP.
'''Thursday'''
'''Thursday'''
-
-Ligation was performed for P2 and GFP.
+
 
-
- We prepared liqued culture for L2 and C2.
+
* Ligation was performed for P2 and GFP.
-
- We tested new compatent cell by RFB transformation.
+
* We prepared liqued culture for L2 and C2.
-
- We prepared kanamycin including plate.
+
* We tested new compatent cell by RFB transformation.
 +
* We prepared kanamycin including plate.
'''Friday'''
'''Friday'''
-
- Single colony isolation was made for C2 and L2.
+
 
-
- C2 and L2 are digested with EcoR1 and Pst1.
+
* Single colony isolation was made for C2 and L2.
-
- electrophoresis was performed for C2 and L2.(Unsuccessful)
+
* C2 and L2 are digested with EcoR1 and Pst1.
-
- Ligation was performed for P2H1 with kanamycin.
+
* electrophoresis was performed for C2 and L2.(Unsuccessful)
-
- We prepared kanamycin including plate.
+
* Ligation was performed for P2H1 with kanamycin.
-
- We prepared liqued culture for P2GFP and L2.
+
* We prepared kanamycin including plate.
-
- Transformation was made for  P2H1.
+
* We prepared liqued culture for P2GFP and L2.
 +
* Transformation was made for  P2H1.
Line 150: Line 163:
'''Saturday'''
'''Saturday'''
-
-Isolation was made for L2 and P2-GFP.After that digestion was made with EcoR1 and Pst1 for these parts.Finally electrophoresis was performed to these parts.The result of P2-GFP was true but  L2 was wrong.
+
 
-
-We prepared 5 liquid culture for P2H1.
+
* Isolation was made for L2 and P2-GFP.After that digestion was made with EcoR1 and Pst1 for these parts.Finally electrophoresis was performed to these parts.The result of P2-GFP was true but  L2 was wrong.
-
-Digestion was made with EcoR1 and Spe1 for P2-GFP
+
* We prepared 5 liquid culture for P2H1.
 +
* Digestion was made with EcoR1 and Spe1 for P2-GFP
'''Sunday'''
'''Sunday'''
-
--Isolation was made  5 coloni for 69h.But microcantifuge is broked.
+
 
-
- We prepared liqued culture for  J04450(400)
+
* Isolation was made  5 coloni for 69h.But microcantifuge is broked.
-
- Transformation was made for  J04450(500-700)
+
* We prepared liqued culture for  J04450(400)
-
-Our parts were renamed.
+
* Transformation was made for  J04450(500-700)
 +
* Our parts were renamed.
Line 164: Line 179:
'''Tuesday'''
'''Tuesday'''
-
- Transformation was made for  J04450(500-700)
+
 
-
-Digestion was made J04450(500-700) EcoR1 and Pst-1.
+
* Transformation was made for  J04450(500-700)
-
-We diluted Lac-1.
+
* Digestion was made J04450(500-700) EcoR1 and Pst-1.
-
- Transformation was made for  Lac-1.
+
* We diluted Lac-1.
-
- electrophoresis was performed for J04450(500-700)
+
* Transformation was made for  Lac-1.
-
-Ligation was performed for 705-79h.
+
* electrophoresis was performed for J04450(500-700)
-
- Transformation was made for  40h,705 and 79h.
+
* Ligation was performed for 705-79h.
 +
* Transformation was made for  40h,705 and 79h.
'''Thursday'''
'''Thursday'''
-
-We made isolation from liquid culture of 40h for testing contamination.Then we made digestion with EcoR1 and Pst1. After that electrophoresis was performed .
+
 
-
-Ligation was made for 40h and 70h.After that transformation was made for these parts.
+
* We made isolation from liquid culture of 40h for testing contamination.Then we made digestion with EcoR1 and Pst1. After that electrophoresis was performed .
-
-We prepared 3 liquid  cultures for each one of LacI,705 and 79h (totally 9 liquid cultures were prepared )
+
* Ligation was made for 40h and 70h.After that transformation was made for these parts.
 +
* We prepared 3 liquid  cultures for each one of LacI,705 and 79h (totally 9 liquid cultures were prepared )
'''Friday'''
'''Friday'''
-
-Isolation was made for LacI,705 and 79h.Then digestion was made with EcoR1 and Pst1 for 705 and 79h , with EcoR1 and Spe1 for LacI.After that electrophoresis was performed for all of these parts.But results werent good.
+
 
 +
* Isolation was made for LacI,705 and 79h.Then digestion was made with EcoR1 and Pst1 for 705 and 79h , with EcoR1 and Spe1 for LacI.After that electrophoresis was performed for all of these parts.But results werent good.
'''Sunday'''
'''Sunday'''
Line 194: Line 212:
'''Monday'''
'''Monday'''
-
- We prepared liqued cultures for W,P,Z,Alpha,Zt and k.
+
* We prepared liqued cultures for W,P,Z,Alpha,Zt and k.
-
- Transformation was made 40hgx,40h and 70h.
+
* Transformation was made 40hgx,40h and 70h.
-
- Digestion was made u1,u2 and u3.(unsuccessful)
+
* Digestion was made u1,u2 and u3.(unsuccessful)
-
- Electrophoresis was performed for u1,u2 and u3.
+
* Electrophoresis was performed for u1,u2 and u3.

Revision as of 22:34, 25 September 2012

Contents

WEEK 1 - June 1st-7th

Friday

Today we started with a briefing from Mustafa where the main action points of the day were discussed. We had been planning the project of this year.We determined our parts that will be necessary:

  • K124014 holin
  • K559010 halorhodopsin+terminator(X2)
  • K112806 endolysine/T4
  • K112808 endolysine/holin/CMV/antiholin

These 4 parts was diluted and tagged. Then we coded these parts:

  • C1:J23100 cons-promoter
  • C2:CMV promoter
  • P1:CL promoter
  • H1:Holorodopsin
  • P2:IPTG
  • L1:endolsin
  • L2:holin
  • l3:eth+antiholin


We prepared 35 plates and 200 ml LB broth for next experiments.

  • Transformation (L1,L2,L3) 

  • C1,C2 streak
  • Coloniese are incubated in liquid culture.(C1)


Saturday

  • Coloniese are incubated liquid culture.( 1,5 ml AMP ) for :

C1(x2),C2,N1,L2,L3.

  • We made this process 2 times because of high mistake risk for first times


Sunday

  • Single colony isolation has made for C1-x,C1-y,C2,L1,L2 and L3.
  • C1-x and C1-y are digested with EcoR1 and Pst1.
  • We prepared liquid culture for C2,L1,L3 again.Because there was not enough DNA for digestion.

Monday

  • Single colony isolation has been made for L1,L2 and L3.
  • Digestion has been made with EcoR1 and Pst1 for L1,L3 and C2.
  • electrophoresis was performed for C1-x,C2,L1,L2 and L3.
  • After electrophoresis,results of L1,L3 was true but the others was wrong.


Tuesday

  • Digestion has been made with Xba1 and Pst1 for L1 and L3.
  • 34 mg/ml chloramphenicol included 49 tubes was prepared.
  • Chloramphenicol included 17 plates was prepared.
  • IPTG induceble promoter was coded as P2.
  • Transformation has been made for H1,L1P2 and L3P2
  • We prepared liquid culture for C1,C2,L2


Wednesday

  • Single colony isolation has been made for C1,C2,L2
  • We prepared liquid culture for C2 again.Because there was not enough DNA for digestion.
  • C1 and L2 are digested.
  • electrophoresis was performed for C1 and L2.
  • The result of C1 was true but the result of L2 was wrong so a new digestion will been performed and after that electrophoresis will been performed for new L2 and old L2.
  • We prepared liquid culture for P2L1,P2L3,C2,H1 and L2.

Thursday

  • We made isolation for P2L1,P2L3,H1,C2,L2 and then digestion has been made with EcoR1 and Pst1 for all of these parts.After that electrophoresis was performed for these parts.
  • The results of P2L1 and P2L3 might be true , we are not sure about this so we need some expert assistance and we need to sequence these part for being sure. Unfortunately the result of L2 was wrong again.
  • We prepared a new liquid culture for L2.


WEEK 2

Friday

  • In order of isoation, digestion and electrophoresis was performed to L2 and C2.By the way electrophoresis was performed 2 times for being sure but both of results were wrong.
  • Digestion has been made with Xba1 and Spe1 for H1.
  • Ligation was performed for P2 and H1 ,C1 and GFP.


WEEK 3

Wednesday

  • Transformation has been made for C2,L2,P2H1 and C1-GFP (unsuccessful)
  • We prepared 200 ml LB broth for next experiments.

Thursday

  • Transformation has been made for C2,L2,P2H1 and C1-GFP.
  • C2 and L2 (successful)

Friday

  • We prepared 200 ml LB broth and 15 plates for next experiments
  • Transformation was made for P2H1 and C1-GFP.
  • We prepared liqued culture for C2 and L2.

Saturday

  • Single colony isolation has been made for C2 and L2.
  • C2 and L2 are digested with EcoR1 and Pst1.


WEEK 4

Monday

  • electrophoresis was performed for C2 and L2.(Unsuccessful)
  • We prepared Tfb1 and Tfb2 for compatent cell.
  • We prepared liquid culture for C2 and L2.

Tuesday

  • Single colony isolation has been made for C2 and L2.
- electrophoresis was performed for C2 and L2.
  • C2 and L2 are digested with EcoR1 and Pst1.


WEEK 5

Monday

  • We added compotent cells to ampicilin included liquid culture and plate.
  • We added compotent cells to cloramphenicoli included plate.
  • We incubated cloramphenicol resistance bacteria to ampicilin included plate.
  • We added compatent cells to plate without antibiotic.

Tuesday

  • We prepared 15 CHL plates.
  • We tested compatent cell by RFB transformation.
  • We prepared liquid culture for preparetion of compatent cell.

Wednesday

  • Transformation was made for C2,L2 and C1-GFP.

Thursday

  • Ligation was performed for P2 and GFP.
  • We prepared liqued culture for L2 and C2.
  • We tested new compatent cell by RFB transformation.
  • We prepared kanamycin including plate.

Friday

  • Single colony isolation was made for C2 and L2.
  • C2 and L2 are digested with EcoR1 and Pst1.
  • electrophoresis was performed for C2 and L2.(Unsuccessful)
  • Ligation was performed for P2H1 with kanamycin.
  • We prepared kanamycin including plate.
  • We prepared liqued culture for P2GFP and L2.
  • Transformation was made for P2H1.


WEEK 6

Saturday

  • Isolation was made for L2 and P2-GFP.After that digestion was made with EcoR1 and Pst1 for these parts.Finally electrophoresis was performed to these parts.The result of P2-GFP was true but L2 was wrong.
  • We prepared 5 liquid culture for P2H1.
  • Digestion was made with EcoR1 and Spe1 for P2-GFP

Sunday

  • Isolation was made 5 coloni for 69h.But microcantifuge is broked.
  • We prepared liqued culture for J04450(400)
  • Transformation was made for J04450(500-700)
  • Our parts were renamed.


WEEK 7

Tuesday

  • Transformation was made for J04450(500-700)
  • Digestion was made J04450(500-700) EcoR1 and Pst-1.
  • We diluted Lac-1.
  • Transformation was made for Lac-1.
  • electrophoresis was performed for J04450(500-700)
  • Ligation was performed for 705-79h.
  • Transformation was made for 40h,705 and 79h.

Thursday

  • We made isolation from liquid culture of 40h for testing contamination.Then we made digestion with EcoR1 and Pst1. After that electrophoresis was performed .
  • Ligation was made for 40h and 70h.After that transformation was made for these parts.
  • We prepared 3 liquid cultures for each one of LacI,705 and 79h (totally 9 liquid cultures were prepared )

Friday

  • Isolation was made for LacI,705 and 79h.Then digestion was made with EcoR1 and Pst1 for 705 and 79h , with EcoR1 and Spe1 for LacI.After that electrophoresis was performed for all of these parts.But results werent good.

Sunday

  • We prepared liqued cultures for Zt and K.
  • Isolation was made 0,H and U.
  • Digestion was made 0,H and U.
  • Electrophoresis was performed for 0,H and U.
  • Transformation was made W,P,Z,Alpha,Zt,K.
  • We prepared compatent cell and AMP plates


WEEK 8

Monday

  • We prepared liqued cultures for W,P,Z,Alpha,Zt and k.
  • Transformation was made 40hgx,40h and 70h.
  • Digestion was made u1,u2 and u3.(unsuccessful)
  • Electrophoresis was performed for u1,u2 and u3.
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