Team:UNIPV-Pavia/Notebook/Week10

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!|[[Team:UNIPV-Pavia/Notebook/Week13|Week 13]]
!|[[Team:UNIPV-Pavia/Notebook/Week13|Week 13]]
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!|[[Team:UNIPV-Pavia/Notebook/Week14|Week 14]]
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|-
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!|[[Team:UNIPV-Pavia/Notebook/Week15|Week 15]]
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!|[[Team:UNIPV-Pavia/Notebook/Week16|Week 16]]
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!|[[Team:UNIPV-Pavia/Notebook/Week17|Week 17]]
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!|[[Team:UNIPV-Pavia/Notebook/Week18|Week 18]]
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!|[[Team:UNIPV-Pavia/Notebook/Week19|Week 19]]
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!|[[Team:UNIPV-Pavia/Notebook/Week20|Week 20]]
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!|[[Team:UNIPV-Pavia/Notebook/Week21|Week 21]]
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|-
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!|[[Team:UNIPV-Pavia/Notebook/Week22|Week 22]]
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!|[[Team:UNIPV-Pavia/Notebook/Week23|Week 23]]
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'''07/21/08'''
'''07/21/08'''
<br>
<br>
-
*Colony PCR for BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079''': 6 colonies from single colonies plate.
+
*Colony PCR for B0030-C0078-B1006-'''R0079''': 6 colonies from single colonies plate.
{|
{|
-
|[[Image:pv_colonypcr_25_single_col.jpg|thumb|300px|left|BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079''']]
+
|[[Image:pv_colonypcr_25_single_col.jpg|thumb|300px|left|B0030-C0078-B1006-'''R0079''']]
|}
|}
-
*Gel results: all the 6 picked colonies were true positive! we chose the 5th colont to grow a 9 ml overnight culture.
+
*Gel results: all the 6 picked colonies were true positive! we chose the 5th colony to grow a 9 ml overnight culture.
-
*We also infected 9 ml LB + Amp with 30 µl of BBa_J23100-BBa_B0030-BBa_C0040-BBa_B1006-'''BBa_R0040''' and '''BBa_B0030'''-BBa_C0061 glycerol stocks to grow two overnight cultures.
+
*We also infected 9 ml LB + Amp with 30 µl of J23100-B0030-C0040-B1006-'''R0040''' and '''B0030'''-C0061 glycerol stocks to grow two overnight cultures.
*Ligation:
*Ligation:
-
**BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' (1:2 ratio, 40 ng of vector)
+
**J23100-B0030-C0012-'''B1006''' (1:2 ratio, 40 ng of vector)
-
**BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' (30 ng of vector)
+
**B0030-I15009-B1006-'''R0082''' (30 ng of vector)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006
*We incubated ligations at 16°C overnight.
*We incubated ligations at 16°C overnight.
Line 71: Line 83:
*Glycerol stocks/miniprep for:
*Glycerol stocks/miniprep for:
{|cellpadding="20px"
{|cellpadding="20px"
-
|BBa_J23100-BBa_B0030-BBa_C0040-BBa_B1006-'''BBa_R0040'''
+
|J23100-B0030-C0040-B1006-'''R0040'''
-
|'''BBa_B0030'''-BBa_C0061
+
|'''B0030'''-C0061
|-
|-
-
|BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079'''
+
|B0030-C0078-B1006-'''R0079'''
|}
|}
-
*We sent BBa_J23100-BBa_B0030-BBa_C0040-BBa_B1006-'''BBa_R0040''' and BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079''' purified plasmids to Primm for sequencing.
+
*We sent J23100-B0030-C0040-B1006-'''R0040''' and B0030-C0078-B1006-'''R0079''' purified plasmids to Primm for sequencing.
*Plasmid digestion for:
*Plasmid digestion for:
{|cellpadding="20px"
{|cellpadding="20px"
-
|'''BBa_B0030'''-BBa_C0061 (E-S)
+
|'''B0030'''-C0061 (E-S)
-
|BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079''' (E-X)
+
|B0030-C0078-B1006-'''R0079''' (E-X)
|}
|}
Line 92: Line 104:
*Ligation plates showed colonies!We put ligation plates at +4°C.
*Ligation plates showed colonies!We put ligation plates at +4°C.
-
*Ligation for BBa_B0030-BBa_C0061-BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079'''.
+
*Ligation for B0030-C0061-B0030-C0078-B1006-'''R0079'''.
*We incubated ligation at 16°C overnight.
*We incubated ligation at 16°C overnight.
Line 99: Line 111:
'''07/24/08'''
'''07/24/08'''
<br>
<br>
-
*Transformation (1 µl) for BBa_B0030-BBa_C0061-BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079''' ligation. We plated transformed bacteria and incubated plate at 37°C overnight.
+
*Transformation (1 µl) for B0030-C0061-B0030-C0078-B1006-'''R0079''' ligation. We plated transformed bacteria and incubated plate at 37°C overnight.
*Colony PCR for:
*Colony PCR for:
-
**BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006'''
+
**J23100-B0030-C0012-'''B1006'''
-
**BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082'''
+
**B0030-I15009-B1006-'''R0082'''
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006
-
*(We performed one PCR for BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' and BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' with 2 min elongation and another PCR for the remaining two ligations with 3 min elongation).
+
*(We performed one PCR for J23100-B0030-C0012-'''B1006''' and B0030-I15009-B1006-'''R0082''' with 2 min elongation and another PCR for the remaining two ligations with 3 min elongation).
-
{|cellpadding="20px"
+
{|cellpadding="1px"
-
|[[Image:pv_pcr_parallel1.jpg|thumb|300px|left|Thermal cycler working on BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' and BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' colonies: 2 min elongation]]
+
|[[Image:pv_pcr_parallel1.jpg|thumb|300px|left|Thermal cycler working on J23100-B0030-C0012-'''B1006''' and B0030-I15009-B1006-'''R0082''' colonies: 2 min elongation]]
-
|-
+
|[[Image:pv_pcr_parallel2.jpg|thumb|300px|left|Thermal cycler working on B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 and B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 colonies: 3 min elongation]]
-
|[[Image:pv_pcr_parallel2.jpg|thumb|300px|left|Thermal cycler working on **BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 and BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 colonies: 3 min elongation]]
+
|}
|}
-
*Electrophoresis (1.2% agarose) for BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' and BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''':
+
*Electrophoresis (1.2% agarose) for J23100-B0030-C0012-'''B1006''' and B0030-I15009-B1006-'''R0082''':
{|
{|
-
|[[Image:pv_colonypcr_19_32.jpg|thumb|300px|left|Marker 1Kb, blank, BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' (7 lanes), BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' (6 lanes)]]
+
|[[Image:pv_colonypcr_19_32.jpg|thumb|300px|left|Marker 1Kb, blank, J23100-B0030-C0012-'''B1006''' (7 lanes), B0030-I15009-B1006-'''R0082''' (6 lanes)]]
|}
|}
-
*Electrophoresis (1% agarose) for BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 and BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006:
+
*Electrophoresis (1% agarose) for B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 and B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006:
{|
{|
-
|[[Image:pv_colonypcr_34_35.jpg|thumb|300px|left|Marker 1Kb, BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 (7 lanes), BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 (7 lanes)]]
+
|[[Image:pv_colonypcr_34_35.jpg|thumb|300px|left|Marker 1Kb, B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 (7 lanes), B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 (7 lanes)]]
|}
|}
*Gel results:
*Gel results:
-
**BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' 1st colony
+
**J23100-B0030-C0012-'''B1006''' 1st colony
-
**BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' 1st colony
+
**B0030-I15009-B1006-'''R0082''' 1st colony
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 1st and 3rd colony
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 1st and 3rd colony
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 1st and 4th colony
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 1st and 4th colony
 +
 
 +
*We decided to keep two colonies for B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 and B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 ligations because they are important parts for our project and we wanted to be sure they were correct.
-
*We decided to keep two colonies for BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 and BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 ligations because they are important parts for our project and we wanted to be sure they were correct.
+
*The fifth colony of B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 showed an unexpected length...(@_@?) We decided to ignore it. Sequencing results will tell us if we made mistakes in assemblies.
*We infected 9 ml LB + Amp with chosen colonies to grow 6 overnight cultures.
*We infected 9 ml LB + Amp with chosen colonies to grow 6 overnight cultures.
Line 141: Line 154:
<br>
<br>
*Glycerol stocks/miniprep for:
*Glycerol stocks/miniprep for:
-
**BBa_J23100-BBa_B0030-BBa_C0012-'''BBa_B1006''' (1)
+
**J23100-B0030-C0012-'''B1006''' (1)
-
**BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' (1)
+
**B0030-I15009-B1006-'''R0082''' (1)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 (1)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 (1)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 (3)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 (3)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 (1)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 (1)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 (4)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 (4)
*We sent these purified plasmids:
*We sent these purified plasmids:
-
**BBa_B0030-BBa_I15009-BBa_BBa_B1006-'''BBa_R0082''' (1)
+
**B0030-I15009-B1006-'''R0082''' (1)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 (1)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 (1)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006-BBa_R0062 (3)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006-R0062 (3)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 (1)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 (1)
-
**BBa_B0030-BBa_C0051-BBa_B0030-BBa_C0079-'''BBa_B1006'''-BBa_R0051-BBa_B0030-BBa_C0062-BBa_B1006 (4)
+
**B0030-C0051-B0030-C0079-'''B1006'''-R0051-B0030-C0062-B1006 (4)
*to Primm for sequencing.
*to Primm for sequencing.
-
*We put BBa_B0030-BBa_C0061-BBa_B0030-BBa_C0078-BBa_B1006-'''BBa_R0079''' plate at +4°C.
+
*We put B0030-C0061-B0030-C0078-B1006-'''R0079''' plate at +4°C.

Latest revision as of 21:26, 26 October 2008


Home.jpg Home Unipv logo.jpg The Team And.jpg The Project Safety.jpg Biological Safety Dna.png Parts Submitted to the Registry
Laptop.jpg Dry Lab Pipette.jpg Wet Lab Math.gif Modeling Note.jpg Protocols Notebook.gif Activity Notebook



Notebook



Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7
Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14
Week 15 Week 16 Week 17 Week 18 Week 19 Week 20 Week 21
Week 22 Week 23 Week 24



Week 10: 07/21/08 - 07/25/08

07/21/08

  • Colony PCR for B0030-C0078-B1006-R0079: 6 colonies from single colonies plate.
B0030-C0078-B1006-R0079
  • Gel results: all the 6 picked colonies were true positive! we chose the 5th colony to grow a 9 ml overnight culture.
  • We also infected 9 ml LB + Amp with 30 µl of J23100-B0030-C0040-B1006-R0040 and B0030-C0061 glycerol stocks to grow two overnight cultures.
  • Ligation:
    • J23100-B0030-C0012-B1006 (1:2 ratio, 40 ng of vector)
    • B0030-I15009-B1006-R0082 (30 ng of vector)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006
  • We incubated ligations at 16°C overnight.



07/22/08

  • Transformation for the 4 overnight ligations (1 µl). We plated transformed bacteria and incubated plates at 37°C overnight.
  • Glycerol stocks/miniprep for:
J23100-B0030-C0040-B1006-R0040 B0030-C0061
B0030-C0078-B1006-R0079
  • We sent J23100-B0030-C0040-B1006-R0040 and B0030-C0078-B1006-R0079 purified plasmids to Primm for sequencing.
  • Plasmid digestion for:
B0030-C0061 (E-S) B0030-C0078-B1006-R0079 (E-X)
  • Gel run/cut/gel extraction.



07/23/08

  • Ligation plates showed colonies!We put ligation plates at +4°C.
  • Ligation for B0030-C0061-B0030-C0078-B1006-R0079.
  • We incubated ligation at 16°C overnight.



07/24/08

  • Transformation (1 µl) for B0030-C0061-B0030-C0078-B1006-R0079 ligation. We plated transformed bacteria and incubated plate at 37°C overnight.
  • Colony PCR for:
    • J23100-B0030-C0012-B1006
    • B0030-I15009-B1006-R0082
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006
  • (We performed one PCR for J23100-B0030-C0012-B1006 and B0030-I15009-B1006-R0082 with 2 min elongation and another PCR for the remaining two ligations with 3 min elongation).
Thermal cycler working on J23100-B0030-C0012-B1006 and B0030-I15009-B1006-R0082 colonies: 2 min elongation
Thermal cycler working on B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 and B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 colonies: 3 min elongation
  • Electrophoresis (1.2% agarose) for J23100-B0030-C0012-B1006 and B0030-I15009-B1006-R0082:
Marker 1Kb, blank, J23100-B0030-C0012-B1006 (7 lanes), B0030-I15009-B1006-R0082 (6 lanes)
  • Electrophoresis (1% agarose) for B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 and B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006:
Marker 1Kb, B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 (7 lanes), B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 (7 lanes)
  • Gel results:
    • J23100-B0030-C0012-B1006 1st colony
    • B0030-I15009-B1006-R0082 1st colony
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 1st and 3rd colony
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 1st and 4th colony
  • We decided to keep two colonies for B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 and B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 ligations because they are important parts for our project and we wanted to be sure they were correct.
  • The fifth colony of B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 showed an unexpected length...(@_@?) We decided to ignore it. Sequencing results will tell us if we made mistakes in assemblies.
  • We infected 9 ml LB + Amp with chosen colonies to grow 6 overnight cultures.



07/25/08

  • Glycerol stocks/miniprep for:
    • J23100-B0030-C0012-B1006 (1)
    • B0030-I15009-B1006-R0082 (1)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 (1)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 (3)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 (1)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 (4)
  • We sent these purified plasmids:
    • B0030-I15009-B1006-R0082 (1)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 (1)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006-R0062 (3)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 (1)
    • B0030-C0051-B0030-C0079-B1006-R0051-B0030-C0062-B1006 (4)
  • to Primm for sequencing.
  • We put B0030-C0061-B0030-C0078-B1006-R0079 plate at +4°C.
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