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Team:Stockholm/1 July 2010
From 2010.igem.org
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== Isolation of requested parts == | == Isolation of requested parts == | ||
Our three requested parts BBa_J18930 (mCerulean; CFP), BBa_J18931 (mCitrine; YFP) and BBa_J18932 (mCherry; RFP) arrived as agar stabs. These were plated onto Amp plates according to [http://partsregistry.org/Help:Requesting_Parts_2009#Using_agar_stabs Registry instructions]. | Our three requested parts BBa_J18930 (mCerulean; CFP), BBa_J18931 (mCitrine; YFP) and BBa_J18932 (mCherry; RFP) arrived as agar stabs. These were plated onto Amp plates according to [http://partsregistry.org/Help:Requesting_Parts_2009#Using_agar_stabs Registry instructions]. | ||
| + | |||
| + | |||
| + | =Maya= | ||
| + | |||
| + | 1 Microarrays - reliability | ||
| + | - How reliable is the protein regulation profile in the article "Transcriptional profiling of melanocytes..." | ||
| + | |||
| + | 2 How should one priorate different types of protein-protein interactions? | ||
| + | Focus on experimental (not predictive ) data and focus first of all at physical PPI second at co expression and co localisation. Skip the rest. | ||
| + | |||
| + | To improve PPI reliability | ||
| + | * Find a good coverage from many primary databases. -How many and with? | ||
| + | * What experiments were used? If the same result is dereved from many different experiments then the PPI is more reliable. | ||
| + | * Look at 3D structures...? | ||
| + | Compare with canonical pathways to get a better insight in the functional roles of the proteins in the network. | ||
Revision as of 15:30, 3 July 2010
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Contents |
Andreas
Preparation of competent BL21(DE3) cells
Competent cells were prepared as previously described.
- Modifications
- Growth temperature was changed to 37°C
- Final OD(600) was 0.57
Preparation of LB agar plates with antibiotics
- 50 ug/ml Km (20 plates)
- 50 ug/ml Amp & 25 ug/ml Cm (10 plates)
- 50 ug/ml Amp & 25 ug/ml Km (10 plates)
Plates were tested by plating with competent, non-transformed Top10 cells
Transformations
Several different transformations were performed. Top10 cells were transformed with pSB1x3 BioBrick vectors and grown on agar plates with appropriate antibiotic(s). BL21(DE3) cells were transformed with SOD- and yCCS-carrying pEX vectors as well as with the pMA vector to test cell competence and grown on Amp plates:
Top10
- pSB1A3.BBa_J04450
- pSB1C3.BBa_J04450
- pSB1K3.BBa_J04450
- pSB1AC3.BBa_J04450
- pSB1AK3.BBa_J04450
BL21(DE3)
- pEX.SOD
- pEX.yCCS
- pMA.BBa_K157011
Isolation of requested parts
Our three requested parts BBa_J18930 (mCerulean; CFP), BBa_J18931 (mCitrine; YFP) and BBa_J18932 (mCherry; RFP) arrived as agar stabs. These were plated onto Amp plates according to [http://partsregistry.org/Help:Requesting_Parts_2009#Using_agar_stabs Registry instructions].
Maya
1 Microarrays - reliability - How reliable is the protein regulation profile in the article "Transcriptional profiling of melanocytes..."
2 How should one priorate different types of protein-protein interactions? Focus on experimental (not predictive ) data and focus first of all at physical PPI second at co expression and co localisation. Skip the rest.
To improve PPI reliability
- Find a good coverage from many primary databases. -How many and with?
- What experiments were used? If the same result is dereved from many different experiments then the PPI is more reliable.
- Look at 3D structures...?
Compare with canonical pathways to get a better insight in the functional roles of the proteins in the network.
