Team:Evry/Notebook/Interlabstudy/Week7

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The major part of the DNA was lost during the purification because the amount of was to weak to be purified from gel. So we decide do transform ''E. coli'' to isolate a  colony containing the desired plasmid for BBa_E0240 and BBa_I20260.
<h2> 08.15.2014 </h2>
<h2> 08.15.2014 </h2>
-
 
+
BBa_E0240 and BBa_I20260 are respectively into a PSB1C3 and a PSB1K3 vector. In order to select colonies, LB complemented with kanamycin or chloramphenicol are necessary.
<h2> 08.16.2014 </h2>
<h2> 08.16.2014 </h2>
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+
Nothing had grown during the night on both plates. Taking into consideration different hypothesis, the transformation was repeated with some changes.
<h2> 08.17.2014 </h2>
<h2> 08.17.2014 </h2>
 +
Colonies had grown on plates as followed:

Revision as of 09:55, 18 August 2014

Week 7

Interlab Study

08.12.2014

The 4 needed parts are: BBa_J23101, BBa_J23115, BBa_E0240 and BBa_I20260. Corresponding wells were located on 2014 Distribution kit plates and resuspended with 10 µL steril water. That permits to obtain a DNA concentration around 0.2 ng/µl (according to the registry. Solutions were transferred into 1 ml eppendorf tubes and stored at -20°C.
To amplify fragments, a PCR was performed on the 4 constructions, with the mix described on table 1.

IMAGE
Table 1: PCR mix preparation

Distribution of 49 µl of mix per PCR tube. Application of program IGEM Q5 PCR.
IMAGE
Table 2: IGEM Q5 PCR program thermocycling conditions
Preparation of a 1% agarose gel: 0.56 g of Top Vision agarose (Thermo Scientific) + 50 ml of TAE 1X.Microwave 30s by 30s until agarose total dissolution. Gel was cooling down until to be lukewarm, one BET drop was added. Gel was loaded with 10µl per sample previously added with 2 µl of loading dye 6X, and 5 µl for ladders. Gel running 45 minutes at 100 mV in TAE 1X buffer.
IMAGE
Figure 1: 1% agarose gel of PCR products.

Lane 1: BBa_J23115 PCR product, Lane 2: pBHR1 PCR product, Lane 3 and 6: Purple 2-Log ladder NEB, Lane 4: BBa_E0240 PCR product, Lane 5: BBa_I20260 PCR product, Lane 7: 1 Kb plus Ladder Ogene Ruller and Lane 8: BBa_J23101 PCR product


We expected to obtain one band per PCR sample corresponding to the interesting amplified fragment. For Lane 2, 3 and 6 it was ok. We had the expected profile. By contrast 2 bands were visible, one at the expected size (around 1200 bp) and another around 600 bp. We decided to perform a purification on gel of each bands.

08.13.2014

PCR products were cleaned with the GeneJET purification kit (Thermo Scientific)followed by DNA quantification with the NanoDrop 2000 (Thermo Scientific).

Preparation of a 1% agarose gel: 0.56 g of Top Vision agarose (Thermo Scientific) + 50 ml of TAE 1X. Microwave 30s by 30s until agarose total dissolution Gel was cooling down until to be lukewarm, one BET drop was added. Gel was loaded with 10µl per sample previously added with 2 µl of loading dye 6X, and 5 µl for ladders. Gel running 45 minutes at 100 mV in TAE 1X buffer.
IMAGE
Figure 2: 1% agarose gel of PCR products from 08.12.2014 after PCR clean up. Lane 1 and 7: Purple 2-Log ladder NEB, Lane 2: BBa_J23101 purified PCR product, Lane 3: BBa_J23115 purified PCR product, Lane 4: BBa_E0240 purified PCR product, Lane 5: BBa_I20260 purified PCR product and Lane 6: pBHR1 purified PCR product

Profiles were same as before PCR clean up. To sequence the amplified parts, we decided to a purification of fragments from the gel as presented below.

Preparation of a 1% agarose gel: 0.56 g of Top Vision agarose (Thermo Scientific) + 50 ml of TAE 1X. Microwave 30s by 30s until agarose total dissolution. Gel was cooling down until to be lukewarm, one BET drop was added. Gel was loaded with 30 µl of BBa_E0240 purified PCR product and BBa_I20260 purified PCR product added with 6 µl of loading dye, at 10µl of the mix per well. Gel running 45 minutes at 100 mV in TAE 1X buffer.
IMAGE
Figure 3: 1% agarose gel of PCR products from 08.12.2014 after PCR clean up. Lane 4 and 8: Purple 2-Log ladder NEB, Lane 1, 2 and 3: BBa_E0240 purified PCR product, Lane 5, 6 and 7: BBa_I20260 purified PCR product

Four pieces of gel were sampled in four tubes to perform a DNA purification from gel.

08.14.2014

To amplify BBa_I20260 and BBa_0240, a PCR was perform with the mix described Table 1. The program IGEM Q5 PCR was applied, see Table 2. PCR products were cleaned with the GeneJET purification kit (Thermo Scientific)followed by DNA quantification with the NanoDrop 2000 (Thermo Scientific).
Preparation of a 1% agarose gel: 0.52 g of Top Vision agarose (Thermo Scientific) + 50 ml of TAE 1X. Microwave 30s by 30s until agarose total dissolution Gel was cooling down until to be lukewarm, one BET drop was added. Gel was loaded with 20 µl of BBa_E0240 PCR product and BBa_I20260 purified PCR product added with 4 µl of loading dye, at 10µl of the mix per well. Gel running 45 minutes at 100 mV in TAE 1X buffer.
IMAGE
Figure 4: 1% agarose gel of PCR products from 08.14.2014 after PCR clean up. Lane 1 and 5: Purple 2-Log ladder NEB, Lane 2, 3 and 4: BBa_E0240 purified PCR product, Lane 6,7 and 8: BBa_I20260 purified PCR product

3 pieces of gel were sampled in four tubes to perform a DNA purification from gel. The DNA purification was made with the GeneJET purification kit (Thermo Scientific.
A verification electrophoresis was performed on a 1% agarose gel.
IMAGE
Figure 5: 1% agarose gel of purified fragments from gel. Lane 1: Purple 2-Log ladder NEB, Lane 2: BBa_E0240 1200 bp purified fragment and Lane 3: BBa_I20260 1200 bp purified fragment
The major part of the DNA was lost during the purification because the amount of was to weak to be purified from gel. So we decide do transform ''E. coli'' to isolate a colony containing the desired plasmid for BBa_E0240 and BBa_I20260.

08.15.2014

BBa_E0240 and BBa_I20260 are respectively into a PSB1C3 and a PSB1K3 vector. In order to select colonies, LB complemented with kanamycin or chloramphenicol are necessary.

08.16.2014

Nothing had grown during the night on both plates. Taking into consideration different hypothesis, the transformation was repeated with some changes.

08.17.2014

Colonies had grown on plates as followed: