Team:Illinois/Antibody Receptor Tyrosine Kinase Fusion Notebook

From 2008.igem.org

(Difference between revisions)
Line 64: Line 64:
6. Resuspend in 10 mL cold 30 mM CaCl2, incubated on ice overnight  
6. Resuspend in 10 mL cold 30 mM CaCl2, incubated on ice overnight  
 +
7. Glycerol added to 10%, cells in freezer
== [https://2008.igem.org/Illinois/19_July_2008 July 19, 2008] ==  
== [https://2008.igem.org/Illinois/19_July_2008 July 19, 2008] ==  
-
Glycerol added to 10%, cells in freezer
 
Transformation:
Transformation:
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3. Ice for 8 minutes
3. Ice for 8 minutes
-
4. Add cells to 1μL LB
+
4. Add cells to 1ml LB
5. Grow for 1 hour
5. Grow for 1 hour
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Master mix already contains MgCl2; should have added extra to some tubes.
Master mix already contains MgCl2; should have added extra to some tubes.
-
PCR program: 1. 94 degrees 5 min
+
PCR program
-
2. 94 degrees 1 min
+
# 94 degrees 5 min
-
3. 50 degrees 1 min
+
# 94 degrees 1 min
-
4. 72 degrees 1 min
+
# 50 degrees 1 min
-
5. GOTO 2. 39 cycles
+
# 72 degrees 1 min
-
6. HOLD at 4 degrees
+
# GOTO 2. 29 cycles
 +
# HOLD at 4 degrees
1.5% agarose gel made, 0.75g agarose in 50ml 0.5X TBE w/10ul EtBr.
1.5% agarose gel made, 0.75g agarose in 50ml 0.5X TBE w/10ul EtBr.
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|}
|}
-
PCR program: 1. 94 degrees 5 min
+
PCR program
-
2. 94 degrees 1 min
+
# 94 degrees 5 min
-
3. 50 degrees 1 min
+
# 94 degrees 1 min
-
4. 72 degrees 1 min
+
# 50 degrees 1 min
-
5. GOTO 2. 29 cycles
+
# 72 degrees 1 min
-
6. HOLD at 4 degrees
+
# GOTO 2. 29 cycles
 +
# 72 degrees 5 min
 +
# HOLD at 4 degrees
Products run on a 1.5% agarose gel, no products of 700-800bp.
Products run on a 1.5% agarose gel, no products of 700-800bp.
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annealing temps: 40, 43.8, 50, 54, 60, and 64 degrees
annealing temps: 40, 43.8, 50, 54, 60, and 64 degrees
-
PCR program: 1. 94 degrees 5 min
+
PCR program
-
2. 94 degrees 1 min
+
# 94 degrees 5 min
-
3. annealing step 1 min
+
# 94 degrees 1 min
-
4. 72 degrees 1 min
+
# annealing step 1 min
-
5. GOTO 2. 29 cycles
+
# 72 degrees 1 min
-
6. HOLD at 4 degrees
+
# GOTO 2. 29 cycles
 +
# HOLD at 4 degrees
PCR products run on 1.5% agarose gel at 200V for ~20 minutes, then 240V for ~20 minutes.
PCR products run on 1.5% agarose gel at 200V for ~20 minutes, then 240V for ~20 minutes.
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== September 25, 2008 ==
+
== [https://2008.igem.org/Illinois/25_September_2008 September 25, 2008] ==
Biobricks
Biobricks
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|}
|}
 +
PCR program
 +
# 94 degrees 4 min
 +
# 94 degrees 1 min
 +
# 50 degrees 1 min
 +
# 72 degrees 3 min
 +
# GOTO 2. 29 cycles
 +
# HOLD at 4 degrees
 +
 +
== [https://2008.igem.org/Illinois/26_September_2008 September 26, 2008] ==
 +
 +
*product from yesterday run on 1% gel, 200V for ~30 minutes
 +
*mostly good results, small amound of DNA for flk-1
 +
*lanes 1,2,6,8,12,14,16,18 cut out and purified with invitrogen gel extraction kit, eluted in 50ul H2O
 +
<br>
 +
[[Image:9_26_08_biobricks.jpg|none]]
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<br>
 +
[[Image:9_26_08_biobricks_(2).jpg|none]]
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 +
PCR to assemble SCA-flk-1 fusion and increase flk-1 yield
 +
 +
{| class="wikitable" border="1"
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|-
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|tube
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|1
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|2
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|3
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|4
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|5
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|6
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|7
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|8
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|9
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|10
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|11
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|12
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|13
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|14
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|15
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|16
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|17
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|18
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|19
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|20
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|-
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|template
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|0.5ul flk-1 A
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|0.5ul flk-1 B
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|0.5ul flk link 1 A
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|0.5ul flk link 1 B
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|0.5ul flk link 2 A
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|0.5ul flk link 2 B
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|0.5ul flk link 3 A
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|0.5ul flk link 3 B
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|0.5ul SCA link + 0.5ul flk link 1
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|0.5ul SCA link + 0.5ul flk link 1 (crude)
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|0.5ul SCA link + 2ul flk link 1
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|0.5ul SCA link + 2ul flk link 1 (crude)
 +
|0.5ul SCA link + 0.5ul flk link 2
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|0.5ul SCA link + 0.5ul flk link 2 (crude)
 +
|0.5ul SCA link + 2ul flk link 2
 +
|0.5ul SCA link + 2ul flk link 2 (crude
 +
|0.5ul SCA link + 0.5ul flk link 3
 +
|0.5ul SCA link + 0.5ul flk link 3 (crude)
 +
|0.5ul SCA link + 2ul flk link 3
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|0.5ul SCA link + 2ul flk link 3 (crude)
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|-
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|primers
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|colspan="20"|1uL forward & reverse for all
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|-
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|mastermix
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|colspan="20"|8.25uL for all
 +
|-
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|H2O
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|colspan="20"|to 50ul total volume
 +
|}
 +
 +
PCR program
 +
# 94 degrees 4 min
 +
# 94 degrees 1 min
 +
# 58 degrees 1 min
 +
# 72 degrees 3 min
 +
# GOTO 2. 29 cycles
 +
# HOLD at 4 degrees
<!-- == Insert Date Here ==
<!-- == Insert Date Here ==

Revision as of 00:55, 17 October 2008

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Contents

July 1, 2008

Made Yeast Media

YPD Medium, per liter:

10g yeast extract

20g peptone

20g dextrose

20g agar(only for plates)

1. Dextrose filter sterilized, the rest autoclaved

2. Weigh nutrients into flask double the volume you want to make, and stir to dissolve

3. Dextrose added to autoclaved media to equivalent of 20 g/L

4. Liquid media placed on bench, plate media placed in 65 degree water bath approximately 5 minutes

5. Poured into plates and allowed to solidify


July 17, 2008

E.Coli Media

LB medium, per liter

10g tryptone

5g yeast extract

5g NaCl

1 mL 1N NaOH

15g (agar for plates)

1. Antibody DNA resuspended in TE buffer, 0.1 μg/μL

2. 5mL LB inoculated with single colony DH5a pro

3. Incubated at 37 degrees overnight


July 18, 2008

Competent cells:

1. 3mL overnight culture of DH5a pro

2. Inoculated into 35mL of LB

3. OD600 checked, want 0.2-0.3

4. Place culture on ice for 3 minutes

5. Spin at 10,000 rpm for 7 minutes, discard supernatant

6. Resuspend in 10 mL cold 30 mM CaCl2, incubated on ice overnight

7. Glycerol added to 10%, cells in freezer

July 19, 2008

Transformation:

1. Cells put in ice 30 min with 1μL plasmid(100ng)

2. Heat Shock for 2 minutes at 42 degrees

3. Ice for 8 minutes

4. Add cells to 1ml LB

5. Grow for 1 hour

6. Plate 100 to 200 μL on LB and amp, grow overnight


July 21, 2008

Observations:

Plenty of colonies on all plates

Also, making 5mL overnight cultures for mini-prep tomorrow.


July 22, 2008

Mini spin prep on LC and HC colonies

Place DNA in 100μL H2O in freezer


July 29, 2008

All primers brought to standard concentration, 30mM

33.3μL H2O added per n mole of primer


July 30, 2008

Assembly PCR: amplify antibody gene fragments and then assemble them, light and heavy chains

tube 1 2 3 4 5 6 7 8
Antibody chain H H L L H H L L
DNA source mini-prep synthesized IDT genes
template 0.5ul
primers 1ul of appropriate forward and reverse primer
MgCl2 3ul 5ul 3ul 5ul 3ul 5ul 3ul 5ul
master mix 20ul
H20 to 50ul total volume

Master mix already contains MgCl2; should have added extra to some tubes.

PCR program

  1. 94 degrees 5 min
  2. 94 degrees 1 min
  3. 50 degrees 1 min
  4. 72 degrees 1 min
  5. GOTO 2. 29 cycles
  6. HOLD at 4 degrees

1.5% agarose gel made, 0.75g agarose in 50ml 0.5X TBE w/10ul EtBr.

20ul of PCR produts loaded on gel w/4ul 6X loading buffer, run at 200V for about half an hour.

All lanes had lots of DNA at ~375bp, PCR worked.

07-30-08 AbFrag Gel1.jpg


July 31, 2008

PCR to asemble fragments from yesterday.

tube 1 2 3 4
template from 7-30 PCR 2+3 2+7 6+7 1+8
template 0.5ul of both heavy and light chains
primers 1ul of appropriate forward and reverse primer
MgCl2 0ul 0ul 3ul 3ul
master mix 20ul
H20 to 50ul total volume

PCR program

  1. 94 degrees 5 min
  2. 94 degrees 1 min
  3. 50 degrees 1 min
  4. 72 degrees 1 min
  5. GOTO 2. 29 cycles
  6. 72 degrees 5 min
  7. HOLD at 4 degrees

Products run on a 1.5% agarose gel, no products of 700-800bp.

7 31 08 assembly.jpg


August 1, 2008

PCR troubleshooting of yesterday's reaction: use gradient for annealing temp (40-65 degrees), use more template, leave out end primers

Four series of reactions using a gradient annealing temp were run in addition to a fifth series omitting the end primers.

reaction series A B C D E
template (5+7) from 7-30 PCR 0.5ul 1ul 1.5ul 2ul 1ul
primers 1ul of forward and reverse primers (omitted in E series)
master mix 20ul
H20 to 50ul total volume

annealing temps: 40, 43.8, 50, 54, 60, and 64 degrees

PCR program

  1. 94 degrees 5 min
  2. 94 degrees 1 min
  3. annealing step 1 min
  4. 72 degrees 1 min
  5. GOTO 2. 29 cycles
  6. HOLD at 4 degrees

PCR products run on 1.5% agarose gel at 200V for ~20 minutes, then 240V for ~20 minutes.

Products in the 700-800bp range in all lanes. Perhaps it worked because of using a differnt product from the 7-30 PCR.

8 1 08 assembly gradient.jpg


August 6, 2008

1.5% agarose gel of 8-1 PCR products run to cut out bands. Products A1, B1, C1, and E1 used.

Bands around 800bp cut out for all lanes and invitrogen gel extraction kit used to collect DNA in 50ul H2O.


September 5, 2008

Flk-1 clones from [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=MGC-18600&Template=mgcMouseClones ATCC] streaked onto LB+amp and incubated at 37 degrees.


September 6, 2008

Colonies picked from flk-1 plate and inoculated into 5ml LB+amp, grown at 37 degrees.

Freeze-dried e. coli with YCp50-poly from [http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=87555&Template=vectors ATCC] resuspended in 5ml LB, grown at 37 degrees.


September 7, 2008

Mini spin prep of flk-1 and YCp50-poly cells, plasmids stored in 50ul H2O.


September 25, 2008

Biobricks

Bricks to be made: H chain, L chain, SCA, flk-1


tube 1 2 3 4 5 6 7 8
0.5uL template H chain L chain SCA SCA SCA SCA flk-1 flk-1
IDT IDT A B C E A B
primers 1uL forward & reverse for all
mastermix 8.25uL for all
H2O 39.25uL for all

PCR program

  1. 94 degrees 4 min
  2. 94 degrees 1 min
  3. 50 degrees 1 min
  4. 72 degrees 3 min
  5. GOTO 2. 29 cycles
  6. HOLD at 4 degrees

September 26, 2008

  • product from yesterday run on 1% gel, 200V for ~30 minutes
  • mostly good results, small amound of DNA for flk-1
  • lanes 1,2,6,8,12,14,16,18 cut out and purified with invitrogen gel extraction kit, eluted in 50ul H2O


9 26 08 biobricks.jpg


9 26 08 biobricks (2).jpg

PCR to assemble SCA-flk-1 fusion and increase flk-1 yield

tube 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
template 0.5ul flk-1 A 0.5ul flk-1 B 0.5ul flk link 1 A 0.5ul flk link 1 B 0.5ul flk link 2 A 0.5ul flk link 2 B 0.5ul flk link 3 A 0.5ul flk link 3 B 0.5ul SCA link + 0.5ul flk link 1 0.5ul SCA link + 0.5ul flk link 1 (crude) 0.5ul SCA link + 2ul flk link 1 0.5ul SCA link + 2ul flk link 1 (crude) 0.5ul SCA link + 0.5ul flk link 2 0.5ul SCA link + 0.5ul flk link 2 (crude) 0.5ul SCA link + 2ul flk link 2 0.5ul SCA link + 2ul flk link 2 (crude 0.5ul SCA link + 0.5ul flk link 3 0.5ul SCA link + 0.5ul flk link 3 (crude) 0.5ul SCA link + 2ul flk link 3 0.5ul SCA link + 2ul flk link 3 (crude)
primers 1uL forward & reverse for all
mastermix 8.25uL for all
H2O to 50ul total volume

PCR program

  1. 94 degrees 4 min
  2. 94 degrees 1 min
  3. 58 degrees 1 min
  4. 72 degrees 3 min
  5. GOTO 2. 29 cycles
  6. HOLD at 4 degrees


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