Team:DTU-Denmark-2/Notebook/Lab notes

From 2011.igem.org

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<a name="Week 1"></a><h3><b>Week 1: 04.07.2011 - 10.07.2011</b></h3>
<a name="Week 1"></a><h3><b>Week 1: 04.07.2011 - 10.07.2011</b></h3>
<a name="Week 2"></a><h3><b>Week 2: 11.07.2011 - 17.07.2011</b></h3>
<a name="Week 2"></a><h3><b>Week 2: 11.07.2011 - 17.07.2011</b></h3>
 +
<a name="Wednesday 13.07.2011"></a><h4>Wednesday</h4>
 +
First primers have been ordered, so we are soon ready for lab.
<a name="Week 3"></a><h3><b>Week 3: 18.07.2011 - 24.07.2011</b></h3>
<a name="Week 3"></a><h3><b>Week 3: 18.07.2011 - 24.07.2011</b></h3>
<a name="Tuesday 19.07.2011"></a><h4>Tuesday</h4>
<a name="Tuesday 19.07.2011"></a><h4>Tuesday</h4>
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Got a new batch of primeres today, they need to be diluted and stocked.  
+
We got a new batch of primers today. They need to be diluted and stocked, before they are ready for use.  
-
There were still 5 biobricks we had difficulty in obtaining; SV40+ori, SV40 pA, LacZ, pyrG and pyrG-DR. We tried to run a touch PCR program, where each sample will run with a annealing temperature from 55° to 65° in each cycle.  
+
We have had some difficulty with obtaining 5 of our new biobricks; SV40+ori, SV40 pA, LacZ, pyrG and pyrG-DR. We ran a touch PCR program, where the annealing temperature ran from 55° to 65° for each sample in each cycle.  
<br>
<br>
<br>
<br>
-
<b>The PCR reactions succeed and we got the following biobricks:  </b>
+
<b>The PCR reactions were successful, so following biobricks are ready for Plug'n'Play:  </b>
   
   
<ul>
<ul>
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<br>
<br>
<a name="Tuesday 26.07.2011"></a><h4>Tuesday</h4>
<a name="Tuesday 26.07.2011"></a><h4>Tuesday</h4>
-
Many new biobricks will be amplified today with the new batch of primeres we received yesterday.
+
The new primer batch we recieved yesterday, will be used for amplification of many many many new biobricks today.
<br>
<br>
<br>
<br>
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<a name="Wednesday 27.07.2011"></a><h4>Wednesday</h4>
<a name="Wednesday 27.07.2011"></a><h4>Wednesday</h4>
-
8 PCR reactions done today with both standard and touch PCR on the biobricks that we still have some problems obtaining.  
+
Today we have run both 8 standard and touch PCR reactions on some of the biobricks that we still have difficulties obtaining.  
<br>
<br>
<br>
<br>
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<a name="Week 5"></a><h3><b>Week 5: 01.08.2011 - 07.08.2011</b></h3>
<a name="Week 5"></a><h3><b>Week 5: 01.08.2011 - 07.08.2011</b></h3>
<a name="Monday 01.08.2011"></a><h4>Monday</h4>
<a name="Monday 01.08.2011"></a><h4>Monday</h4>
-
A new week, new energy!
+
New week, new energy!
-
Today we did 15 PCR reactions were conducted including parts for iGEM Copenhagen team and we got 14 correct. The annealing temperature was change to 63° and it worked like magic!  
+
Today 15 PCR reactions were conducted, including parts for iGEM Copenhagen team. 14 succeeded. The annealing temperature was increased to 63°, and it worked like magic!  
<br>
<br>
<br>
<br>
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<br>
<br>
<a name="Thursday 04.08.2011"></a><h4>Thursday</h4>
<a name="Thursday 04.08.2011"></a><h4>Thursday</h4>
-
Today we purified 22 biobricks, which have been obtained over the last week of laboratory work with PCR. The purification of DNA was done by using the illustra GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) according to manufactures manual for purification of DNA from TAE and TBE agarose gels protocol, see protocol section for more information.<br><br>
+
Today we purified 22 biobricks, which have been obtained with PCR during the last week of laboratory work. The purification of DNA was done by using the illustra GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) according to the manufactures manual for purification of DNA from TAE and TBE agarose gels protocol, see protocol section for more information.<br><br>
-
Still have not been able to get biobrick pyrG and pyrG-DR after many many attempts. So we did use some other primers without USER-tails (Which sometimes can be tricky using) and have been used before and are known to work. This was done to verify if there was something wrong with the DNA template. The gel electrophoresis did not show any bands, so we concluded that it is our DNA template that is the source of error with the PCR reaction.  
+
Despite several attempts, we have not been able to obtain biobrick pyrG and pyrG-DR. Therefore we made a test with well-known primers without USER-tails (sometimes these USER-tails can be tricky). This was done to verify if something was wrong with the DNA template. The gel electrophoresis did not show any bands, meaning that the DNA template was the source of error.  
<br>
<br>
<br>   
<br>   
-
Today, we also started cultivation of the two mammalian cell lines, HeLa and U2OS. They were defrosted and cultivated in in DMEM medium containing serum, penicillin and streptomycin. Each cell line was then transferred to a 25 cm2 culture flask, see protocol section.
+
We also started cultivation of the mammalian cell line, U2OS, which is derived from a 15-year old patient with osteosarcoma (bone cancedr). They were defrosted and cultivated in in DMEM medium containing serum, penicillin and streptomycin. The cell line was then transferred to a 25 cm2 culture flask, see protocol section.
<br>
<br>
<br>
<br>
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<a name="Monday 08.08.2011"></a><h4>Monday</h4>
<a name="Monday 08.08.2011"></a><h4>Monday</h4>
-
Today we started out first USER cloning, exciting to see if our system works! <br>
+
Today we made the first USER cloning, it is very exciting to see if our system works! <br>
All our biobricks are divided into devices, see protocol for USER MIX. <br>
All our biobricks are divided into devices, see protocol for USER MIX. <br>
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After new DNA template we finally succeed in getting biobricks pyrG and pyrG-DR.   
After new DNA template we finally succeed in getting biobricks pyrG and pyrG-DR.   
<br>
<br>
-
U2OS cells HeLa cells
+
The U2OS cell line was splitted and passed on to new culture flasks. They looked really lovely in the microscope, which bodes well for future confocal microscopy. They seem to thrive in the mammalian cell lab, and they are passed on every second or third day, depending on the initial cell concentration.
<br>
<br>
<br>
<br>
<a name="Tuesday 09.08.2011"></a><h4>Tuesday</h4>
<a name="Tuesday 09.08.2011"></a><h4>Tuesday</h4>
-
Inoculation of E.coli with USER cloning done the day before.  
+
We inoculated E.coli with the plasmides done by USER cloning yesterday.  
<br>
<br>
<br>
<br>
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<br>
<br>
-
Inser gelphoto 09.08.11 x2
+
Insert gelphoto 09.08.11 x2
<br>
<br>
<br>
<br>
-
<b>Purification with GFX kit on rhe following biobricks:</b>
+
<b>Purification with GFX kit on the following biobricks:</b>
<br>
<br>
<ul>
<ul>
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<br>
<br>
<a name="Wednesday 10.08.2011"></a><h4>Wednesday</h4>
<a name="Wednesday 10.08.2011"></a><h4>Wednesday</h4>
-
U2OS cells HeLa cells
+
The U2OS cells are checked out in the microscope. They had a confluency of about 90%, which means that they are ready to pass on to new culture flasks. This was done according to the protocol (see protocol for passing and maintenance of mammalian cells")
<br>
<br>
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<br>
<br>
<br>
<br>
-
inset gel-photo 12.08.11
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Insert gel-photo 12.08.11
<br>
<br>
<br>
<br>
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<br>
<br>
<a name="Monday 15.08.2011"></a><h4>Monday</h4>
<a name="Monday 15.08.2011"></a><h4>Monday</h4>
-
The U2OS are splitted and passed on to coverslips placed in a 6-well plate and a new 75 cm2 flask. They are placed in the incubator overnight - and tomorrow they will be ready for transfection.
+
The U2OS cells were splitted and passed on to a new 75 cm2 culture flask and to coverslips placed in a 6-well plate. They are placed in the incubator overnight - and tomorrow they will be ready for transfection with plasmides.
<br>
<br>
<a name="Tuesday 16.08.2011"></a><h4>Tuesday</h4>
<a name="Tuesday 16.08.2011"></a><h4>Tuesday</h4>
-
Transfection of U2OS cells.
+
We transfected U2OS cells with plasmides containing GFP and placed them in the incubator.  
<br>
<br>
 +
<a name="Wednesday 17.08.2011"></a><h4>Wednesday</h4>
 +
<br>
 +
<a name="Thursday 18.08.2011"></a><h4>Thursday</h4>
 +
The coverslips covered with transfected U2OS cells were washed and fixated. We put the coverslips upside down on a glass slide and fixated them with nailpolish (very high fashion). We took them on a little journey to building 301 to get confocal pictures of them - and they looked great and green.
 +
<br>
 +
<a name="Friday 19.08.2011"></a><h4>Friday</h4>
 +
<br>
 +
<a name="Week 8"></a><h3><b>Week 8: 22.08.2011 - 28.08.2011</b></h3>
 +
<br>
 +
<a name="Monday 22.08.2011"></a><h4>Monday</h4>
 +
The U2OS cells are splitted and passed on to a new culture flask and to coverslips placed in the bottom of 2 6-well-plates.
 +
<br>
 +
<a name="Tuesday 23.08.2011"></a><h4>Tuesday</h4>
 +
The U2OS cells are transfected with all the mammalian plasmides. So hopefully we will get some really cool pictures soon with cells expressing RFP, CFP, YFP, GFP, and GFP targeted to the peroxisomes.
 +
<br>
 +
<a name="Wednesday 24.08.2011"></a><h4>Wednesday</h4>
 +
The coverslips covered with transfected cells were washed and fixated. We put the coverslips upside down on a glass slide and fixated them with nailpolish. We took them to building 301 for confocal microscopy. The cells looked great - everything worked = we are done with the mammalian cells. Hip hip hurra!
 +
<br>
 +
<a name="Thursday 25.08.2011"></a><h4>Thursday</h4>
 +
<br>
 +
<a name="Friday 26.08.2011"></a><h4>Friday</h4>
<a name="September"></a><h2><b>September</b></h2>
<a name="September"></a><h2><b>September</b></h2>
<a name="October"></a><h2><b>October</b></h2>
<a name="October"></a><h2><b>October</b></h2>

Revision as of 14:51, 6 September 2011




Lab notes

July



Week 1: 04.07.2011 - 10.07.2011

Week 2: 11.07.2011 - 17.07.2011

Wednesday

First primers have been ordered, so we are soon ready for lab.

Week 3: 18.07.2011 - 24.07.2011

Tuesday

First day in the lab and 48 biobricks to go, how exciting!
Of the 48 biobricks we will have when the project is finished we had only established 17 of them and ordered primers. We started the day with 11 PCR reactions of the first bash of 17 biobricks, we still need some DNA templates to due all 17. 6 PCR were correct and was purified with a purification Kit (GE Healthcare). So only 42 biobricks to go!

Biobricks in the bag:
  • pALC
  • TtrpC
  • Terminator 1
  • Terminator 2
  • Terminator 3
  • argB
insert 20.07.2011 07:12

Thursday

Some of the PCR reactions that didn't work Tuesday were repeated with a different annealing temperature and amplification of new biobricks.

New biobricks in the bag:
  • PGK
  • BGHpA
  • eGFP+k_GOI
Insert gel-photo 21.07.2011 14:31

The fragments will be frozen and purified later.

We still have not succeed to make biobricks pyrG and pyrG-DR (use as a marker in fungi), despite two PCR attempts with a high annealing (59°) and low (56°) temperature.

Work for iGEM Copenhagen team
We have established collaboration with iGEM Copenhagen team, where we will create some biobricks for them and they can use our plug 'n' play system and they will save a lot of time. So today we transformed competent E.coli cells with some of the standard biological parts from iGEM, BBa_R0010, Bba_B0015 and BBa_J52034, so we later take make biobricks to match our system.

Friday

The biobrick which we still have not succeed in making with PCR is tried again with small modification, adding MgCl2 50mM to the reactions.

Biobrick obtained:
  • CMV
  • hygR
insert 22.07.11 12:11 insert 22.07.11 12:27

The fragments will be frozen and purified later.

Week 4: 25.07.2011 - 31.07.2011


Monday

We got a new batch of primers today. They need to be diluted and stocked, before they are ready for use. We have had some difficulty with obtaining 5 of our new biobricks; SV40+ori, SV40 pA, LacZ, pyrG and pyrG-DR. We ran a touch PCR program, where the annealing temperature ran from 55° to 65° for each sample in each cycle.

The PCR reactions were successful, so following biobricks are ready for Plug'n'Play:
  • SV40 +ori
  • SV40 pA
  • LacZ
Insert of gel photo 26.07.11 11:45 The fragments will be frozen and purified later. We still have trouble with obtaining pyrG and pyrG-DR.

Tuesday

The new primer batch we recieved yesterday, will be used for amplification of many many many new biobricks today.

Out of 15 PCR reactions only 5 succeeded:
  • GFP_GOI
  • GFP_modul
  • GFP_TS
  • eGFP_TS
  • eGFP_module
Insert gel photo 26.07.11 16:24

Wednesday

Today we have run both 8 standard and touch PCR reactions on some of the biobricks that we still have difficulties obtaining.

Only one succeeded:
  • hgH-polyA
Insert 27/7-11

August


Week 5: 01.08.2011 - 07.08.2011

Monday

New week, new energy! Today 15 PCR reactions were conducted, including parts for iGEM Copenhagen team. 14 succeeded. The annealing temperature was increased to 63°, and it worked like magic!

New biobricks in the bag:
  • RFP_GOI
  • RFP_modul
  • RFP_TS
  • bleR
  • pgpdA
  • yA
  • Plasmid_fun
  • Plasmid_Mam
  • Amp
  • Hygromycin
  • CYP79A2 (Copenhagen part)
  • Terminator (Copenhagen part)
  • pIPTG (Copenhagen part)
  • CYP79B2(Copenhagen part)

Wednesday

We still have 3 biobricks we haven’t been able to obtain with PCR: Neomycin, pyrG and pyrG-DR.
Today we tried again with gradient PCR to find the optimal melting temperature. We were only one new biobrick:
  • Neomycin
Insert gel photo 03.08.11 16:24

Thursday

Today we purified 22 biobricks, which have been obtained with PCR during the last week of laboratory work. The purification of DNA was done by using the illustra GFX PCR DNA and Gel Band Purification Kit (GE Healthcare) according to the manufactures manual for purification of DNA from TAE and TBE agarose gels protocol, see protocol section for more information.

Despite several attempts, we have not been able to obtain biobrick pyrG and pyrG-DR. Therefore we made a test with well-known primers without USER-tails (sometimes these USER-tails can be tricky). This was done to verify if something was wrong with the DNA template. The gel electrophoresis did not show any bands, meaning that the DNA template was the source of error.

We also started cultivation of the mammalian cell line, U2OS, which is derived from a 15-year old patient with osteosarcoma (bone cancedr). They were defrosted and cultivated in in DMEM medium containing serum, penicillin and streptomycin. The cell line was then transferred to a 25 cm2 culture flask, see protocol section.

Week 5: 08.08.2011 - 14.08.2011


Monday

Today we made the first USER cloning, it is very exciting to see if our system works!
All our biobricks are divided into devices, see protocol for USER MIX.

The following devices were cloned today:
  • Device 1: plasmid_mam (30) + CMV (3) + eGFP (32) + Hgh pA (33) + Hygromycin (18)
  • Device 2: plasmid_mam (30) + SV40 (2) + eGFP (32) + SV40 pA (4) + Hygromycin (18)
  • Device 3: plasmid_mam (30) + PGK (1) + eGFP (32) + BGH pA (5) + Neomycin (19)
  • Device 4: plasmid_fun (28) + pAlc (7) + LacZ (8) + T1 (14) + argB (17)
  • Device 5: plasmid_fun (28) + gpdA (26) + GFP (24) + trpC (13) + hygR (12)
  • Device 6: plasmid_fun (28) + gpdA (26) + RFP (21) + trpC (13) + hygR (12)
  • Device 7: plasmid_mam (30) + pIPTG (C2) + CYP79B2 (C5) + Terminator (C6) + amp (C1)
  • Device 8: plasmid_mam (30) + pIPTG (C2) + CYP79A2 (C4) + Terminator (C6) + amp (C1)

PCR reactions done today:
  • eGFP+k_GOI (6)
  • eGFP_TS (31)
  • yA (27)
  • GFP_TS (25)
  • RFP_TS (22)
  • RFP_GOI (20)
  • MTS (34)
  • GFP_PTS1_fun (35)
  • GFP_PTS1_mam (36)
  • RFP_NLS_module (37)
  • pyrG (10)
  • pyrG-DR (11)
insert gel photo 08.08.11

After new DNA template we finally succeed in getting biobricks pyrG and pyrG-DR.
The U2OS cell line was splitted and passed on to new culture flasks. They looked really lovely in the microscope, which bodes well for future confocal microscopy. They seem to thrive in the mammalian cell lab, and they are passed on every second or third day, depending on the initial cell concentration.

Tuesday

We inoculated E.coli with the plasmides done by USER cloning yesterday.

PCR done today:
  • RFP_TS
  • RFP_GOI
  • RFP_NLS_Module
  • nr.37

Insert gelphoto 09.08.11 x2

Purification with GFX kit on the following biobricks:
  • nr.6
  • nr. 31
  • nr.27
  • nr.25
  • nr.22
  • nr.34
  • nr.35
  • nr.36
  • nr.20
  • nr.37
  • nr.10
  • nr.11

USER cloning done today:
  • Device 9: plasmid_fun (28) + xxx (26) + xxx (34) + xxx (25) + xxx (13) + xxx (12)
  • Device 10: plasmid_fun (28) + xxx (26) + xxx (35) + xxx (13) + xxx (12)
  • Device 11: plasmid_fun (28) + xxx (26) + xxx (37) + xxx (13) + xxx (12)
  • Device 12: plasmid_mam (30) + xxx (3) + xxx (36) + xxx (5) + xxx (18)
  • Device 13: plasmid_mam (30) + xxx (3) + xxx (32) + xxx (32) + xxx (18)

Wednesday

The U2OS cells are checked out in the microscope. They had a confluency of about 90%, which means that they are ready to pass on to new culture flasks. This was done according to the protocol (see protocol for passing and maintenance of mammalian cells")

Friday

Today we did 13 PCR reaction, some of them includes parts to characterise our two promoters pAlc and DMKP-P6 and some parts for iGEM Copenhagen team.

  • GFP_GOI (23)
  • GFP_PTS_fun (35)
  • GFP_PTS_mam (36)
  • RFP_NLS (37)
  • DMKP_P6 (38)
  • ptrA (40)
  • 1A2 (C7)
  • 2C9 (C8)
  • pAlc-L (B1)
  • DMKP_P6-L (B3)
  • RFP_TS (22)
  • RFP_GOI (20)


Insert gel-photo 12.08.11

The U2OS cells are splitted and passed on to two new 75 cm2 culture flasks. Hopefully, they will be ready to pass on to cover slips on monday.

Week 7: 15.08.2011 - 21.08.2011


Monday

The U2OS cells were splitted and passed on to a new 75 cm2 culture flask and to coverslips placed in a 6-well plate. They are placed in the incubator overnight - and tomorrow they will be ready for transfection with plasmides.

Tuesday

We transfected U2OS cells with plasmides containing GFP and placed them in the incubator.

Wednesday


Thursday

The coverslips covered with transfected U2OS cells were washed and fixated. We put the coverslips upside down on a glass slide and fixated them with nailpolish (very high fashion). We took them on a little journey to building 301 to get confocal pictures of them - and they looked great and green.

Friday


Week 8: 22.08.2011 - 28.08.2011


Monday

The U2OS cells are splitted and passed on to a new culture flask and to coverslips placed in the bottom of 2 6-well-plates.

Tuesday

The U2OS cells are transfected with all the mammalian plasmides. So hopefully we will get some really cool pictures soon with cells expressing RFP, CFP, YFP, GFP, and GFP targeted to the peroxisomes.

Wednesday

The coverslips covered with transfected cells were washed and fixated. We put the coverslips upside down on a glass slide and fixated them with nailpolish. We took them to building 301 for confocal microscopy. The cells looked great - everything worked = we are done with the mammalian cells. Hip hip hurra!

Thursday


Friday

September

October

November

Retrieved from "http://2011.igem.org/Team:DTU-Denmark-2/Notebook/Lab_notes"