Lab Notebook

From 2007.igem.org

(Difference between revisions)
(→August 21st, 2007)
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== August 21st, 2007 ==
+
== August 21, 2007 ==
Start Time: 11:00 am
Start Time: 11:00 am
• Charles showed me how to use the registry properly so if anyone needs to know  how to use the registry properly just let me know.
• Charles showed me how to use the registry properly so if anyone needs to know  how to use the registry properly just let me know.
-
o We searched for super parts which is more like a couple of parts ligated together so that it makes our job a hell lot easier
+
 
 +
o We searched for super parts which is more like a couple of parts ligated together so that it makes our job a lot easier
 +
 
o So we chose 7 parts to be transformed from the neural network MODIFIED model
o So we chose 7 parts to be transformed from the neural network MODIFIED model
 +
• Part timer Muhammad Talal Latif showed up and I instructed him on how to do transformation properly
• Part timer Muhammad Talal Latif showed up and I instructed him on how to do transformation properly
• So I used 20 l of TE buffer to extract:
• So I used 20 l of TE buffer to extract:
 +
o J 37033: 8F, Plate:3 (Amp Res)
o J 37033: 8F, Plate:3 (Amp Res)
 +
o S 01640: 3L, Plate:3 (Amp Res)
o S 01640: 3L, Plate:3 (Amp Res)
 +
• Both of them were from the iGEM 2007 Kit Plates
• Both of them were from the iGEM 2007 Kit Plates
 +
• We stored the plasmids in the –20C freezer labeled in red DNA remaining
• We stored the plasmids in the –20C freezer labeled in red DNA remaining
 +
• Added 4 l  of J37033 and S01640 to separate competent cell (DH5Z1) eppendorf tubes from the –80C freezer
• Added 4 l  of J37033 and S01640 to separate competent cell (DH5Z1) eppendorf tubes from the –80C freezer
 +
• So now we are following the Transformation steps from the guidelines posted
• So now we are following the Transformation steps from the guidelines posted
 +
• We used two AMP plates made from before
• We used two AMP plates made from before
-
 
• We also made 8 AMP plates where 4 is going to be used today for the other four parts which we also transformed:
• We also made 8 AMP plates where 4 is going to be used today for the other four parts which we also transformed:
 +
o I 13507: (Used form 2005 stock) (AMP Res)
o I 13507: (Used form 2005 stock) (AMP Res)
 +
o S 01003: 20O, Plate:1 (AMP Res)
o S 01003: 20O, Plate:1 (AMP Res)
 +
o J 23100: 21E, Plate: 3 (AMP Res)
o J 23100: 21E, Plate: 3 (AMP Res)
 +
o S 01414: 22O, Plate: 1 (AMP Res)
o S 01414: 22O, Plate: 1 (AMP Res)
• We also made 3 AMP and KAN plates where 1 is going to be used:
• We also made 3 AMP and KAN plates where 1 is going to be used:
 +
o F 1610: 1B, Plate: 2, (AMP and KAN Resistant)
o F 1610: 1B, Plate: 2, (AMP and KAN Resistant)
• CONFUSION: While making the AMP and KAN plates we used AMP of 100mg/ml whereas KAN was 30mg/ml. So even though KAN was of different concentration we used the same quantity.
• CONFUSION: While making the AMP and KAN plates we used AMP of 100mg/ml whereas KAN was 30mg/ml. So even though KAN was of different concentration we used the same quantity.
 +
o CHARLES AND ANDY GIVE US SOME INSIGHT ON TO THIS TOPIC
o CHARLES AND ANDY GIVE US SOME INSIGHT ON TO THIS TOPIC
• So we left all 7 plates for overnight incubation and hopefully we see some results tomorrow
• So we left all 7 plates for overnight incubation and hopefully we see some results tomorrow
-
 
• Everybody please welcome SeungMe (part time) who came in and helped me finish the work today and of course Charles
• Everybody please welcome SeungMe (part time) who came in and helped me finish the work today and of course Charles
 +
 +
== August 22, 2007 ==
 +
 +
Start Time: 5:30 pm – End Time: 7:30 pm
 +
Members Present: Yusuf, Anam
 +
 +
• We did Mini Prep overnight and since I did 7 transformations, we decided to do 4 copies of each labeled A,B,C,D so that we have more flexibility in choosing our parts properly.
 +
• These are the following symbols we used to clarify all the tubes with the parts
 +
 +
Black circle - I 13507 (AMP Res) (A – D)
 +
 +
Red circle - F 1610 (AMP & KAN Res) (A – D)
 +
 +
Green Dot - S 01640 (AMP Res) (A – D)
 +
 +
Black dot - S 01414 (AMP Res) (A – D)
 +
 +
Red dot - J 37033 (AMP Res) (A – D)
 +
 +
Black line - J 23100 which is a promoter (AMP Res) (A – D)
 +
 +
Red line - S 01003 (AMP Res) (A – D)
 +
 +
• We also labeled our colonies from the Agar plates which were chosen for miniprep overnight  as it was instructed by Seema to both Anam and Esther.
 +
• The cells which had the promoter J 23100 were light pink colored if Charles and Andy would like to shed some light upon that that would be great.
 +
 +
== August 23, 2007 ==
 +
 +
Start time: 6:30pm
 +
 +
F/T: Anam
 +
 +
P/T: Fareeha
 +
 +
 +
-Done length check PD for all of A, green circle B, red circle B, black dot B
 +
 +
-Enzymes X and P used for all except for J23100 because the part is too small and so the plasmid that contained it was linearized using enzyme P.
 +
 +
-Buffer 2 was used.
 +
 +
Results:
 +
 +
-All were correct length except for samples from colonies A and B of F1610 and colony A of J37033.
 +
 +
- S01003 (colony A), S01414 (colony B), I13507 (colony A) had 3 bands.
 +
 +
- The 3rd band might have shown up because some of the plasmid was only cut in one location.
 +
 +
To do list:
 +
 +
1) Do a PD length check for the rest of the samples
 +
 +
2) Discuss with Yusuf how much information needs to be recorded when observing the bands in a gel for PD length check
 +
 +
Note: There is one gel left in the fridge. It was made today.
 +
 +
== August 24, 2007 ==
 +
 +
Time: 5 pm
 +
 +
F/T: Anam
 +
 +
P/T: Talal
 +
 +
 +
-Record the results of the gel Yusuf had made and run (included in table below)
 +
 +
-PD length check for J23100 colony C successful.
 +
 +
-1 band between 6 and 7 on gel
 +
 +
 +
== August 27, 2007 ==
 +
 +
Start Time: 11:00 pm – End Time: 3:00 pm
 +
 +
Members Present: Yusuf, Mimi, Talal
 +
 +
 +
• Carried out plasmid digest (length checks) on I 13507 B and J 37033 B
 +
 +
• '''Length Check results:'''
 +
 +
''I 13507 B – Overall 3 bands were seen for this plasmid''
 +
 +
6-7 (Closer to 7 than to 6)
 +
 +
8-9 (Closer to 9 than to 8)
 +
 +
11-12 (Closer to 11 than to 12)
 +
 +
The number of parts and parts and plasmid match up closely but the first band between 6-7 could be of the uncut plasmid
 +
 +
 +
''J 37033 B – Overall 2 bands were seen''
 +
 +
8-9 (Closer to 9 than to 8)
 +
 +
10-11 (In the middle)
 +
 +
The bands formed doesn’t match up with the given numbers for its part and plasmid from the registry
 +
 +
 +
• Did Mini-prep overnight for F 1610  with 4 colonies labeled A', B', C', D' and put it in the incubator

Revision as of 20:19, 27 August 2007

Contents

August 21, 2007

Start Time: 11:00 am

• Charles showed me how to use the registry properly so if anyone needs to know how to use the registry properly just let me know.

o We searched for super parts which is more like a couple of parts ligated together so that it makes our job a lot easier

o So we chose 7 parts to be transformed from the neural network MODIFIED model

• Part timer Muhammad Talal Latif showed up and I instructed him on how to do transformation properly

• So I used 20 l of TE buffer to extract:

o J 37033: 8F, Plate:3 (Amp Res)

o S 01640: 3L, Plate:3 (Amp Res)

• Both of them were from the iGEM 2007 Kit Plates

• We stored the plasmids in the –20C freezer labeled in red DNA remaining

• Added 4 l of J37033 and S01640 to separate competent cell (DH5Z1) eppendorf tubes from the –80C freezer

• So now we are following the Transformation steps from the guidelines posted

• We used two AMP plates made from before

• We also made 8 AMP plates where 4 is going to be used today for the other four parts which we also transformed:

o I 13507: (Used form 2005 stock) (AMP Res)

o S 01003: 20O, Plate:1 (AMP Res)

o J 23100: 21E, Plate: 3 (AMP Res)

o S 01414: 22O, Plate: 1 (AMP Res)

• We also made 3 AMP and KAN plates where 1 is going to be used:

o F 1610: 1B, Plate: 2, (AMP and KAN Resistant)


• CONFUSION: While making the AMP and KAN plates we used AMP of 100mg/ml whereas KAN was 30mg/ml. So even though KAN was of different concentration we used the same quantity.

o CHARLES AND ANDY GIVE US SOME INSIGHT ON TO THIS TOPIC

• So we left all 7 plates for overnight incubation and hopefully we see some results tomorrow

• Everybody please welcome SeungMe (part time) who came in and helped me finish the work today and of course Charles

August 22, 2007

Start Time: 5:30 pm – End Time: 7:30 pm Members Present: Yusuf, Anam

• We did Mini Prep overnight and since I did 7 transformations, we decided to do 4 copies of each labeled A,B,C,D so that we have more flexibility in choosing our parts properly. • These are the following symbols we used to clarify all the tubes with the parts

Black circle - I 13507 (AMP Res) (A – D)

Red circle - F 1610 (AMP & KAN Res) (A – D)

Green Dot - S 01640 (AMP Res) (A – D)

Black dot - S 01414 (AMP Res) (A – D)

Red dot - J 37033 (AMP Res) (A – D)

Black line - J 23100 which is a promoter (AMP Res) (A – D)

Red line - S 01003 (AMP Res) (A – D)

• We also labeled our colonies from the Agar plates which were chosen for miniprep overnight as it was instructed by Seema to both Anam and Esther. • The cells which had the promoter J 23100 were light pink colored if Charles and Andy would like to shed some light upon that that would be great.

August 23, 2007

Start time: 6:30pm

F/T: Anam

P/T: Fareeha


-Done length check PD for all of A, green circle B, red circle B, black dot B

-Enzymes X and P used for all except for J23100 because the part is too small and so the plasmid that contained it was linearized using enzyme P.

-Buffer 2 was used.

Results:

-All were correct length except for samples from colonies A and B of F1610 and colony A of J37033.

- S01003 (colony A), S01414 (colony B), I13507 (colony A) had 3 bands.

- The 3rd band might have shown up because some of the plasmid was only cut in one location.

To do list:

1) Do a PD length check for the rest of the samples

2) Discuss with Yusuf how much information needs to be recorded when observing the bands in a gel for PD length check

Note: There is one gel left in the fridge. It was made today.

August 24, 2007

Time: 5 pm

F/T: Anam

P/T: Talal


-Record the results of the gel Yusuf had made and run (included in table below)

-PD length check for J23100 colony C successful.

-1 band between 6 and 7 on gel


August 27, 2007

Start Time: 11:00 pm – End Time: 3:00 pm

Members Present: Yusuf, Mimi, Talal


• Carried out plasmid digest (length checks) on I 13507 B and J 37033 B

• Length Check results:

I 13507 B – Overall 3 bands were seen for this plasmid

6-7 (Closer to 7 than to 6)

8-9 (Closer to 9 than to 8)

11-12 (Closer to 11 than to 12)

The number of parts and parts and plasmid match up closely but the first band between 6-7 could be of the uncut plasmid


J 37033 B – Overall 2 bands were seen

8-9 (Closer to 9 than to 8)

10-11 (In the middle)

The bands formed doesn’t match up with the given numbers for its part and plasmid from the registry


• Did Mini-prep overnight for F 1610 with 4 colonies labeled A', B', C', D' and put it in the incubator

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