Difference between revisions of "Project:Plant species testing"

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We are using primers for plants to test and refine our DNA extraction / PCR technique. First project is to test for peas. Inspiration and primers are in this [http://www.epochlifescience.com/Product/SpinColumn/EconoSpin%20Plant%20Seed%20gDNA.pdf paper].
 
We are using primers for plants to test and refine our DNA extraction / PCR technique. First project is to test for peas. Inspiration and primers are in this [http://www.epochlifescience.com/Product/SpinColumn/EconoSpin%20Plant%20Seed%20gDNA.pdf paper].
  
== First extraction and PCR - 17/7/12 ==
+
== 1st attempt - 17 and 18/7/12 ==
  
We used two methods of extraction. Method 1:
+
Extraction (From [http://www.springerlink.com/content/n6293v8808n5g836/ this] paper - we also have full text available):
 
 
* Blend peas with salt and detergent according to [http://learn.genetics.utah.edu/content/labs/extraction/howto/ this] protocol. Sieve.
 
* Incubate for 15 mins at 60°C (optional step that we didn't take)
 
* Centrifuge - recover supernatant
 
* Add proteinease K (100 ul of 1mg / ml solution to 300 ul of pea template) - incubate for 1 hr at 50C (action of proteinase k) then 94 C for 10 mins (inactivation of proteinase K)
 
* Precipitation to follow
 
 
 
Method 2 (From [http://www.springerlink.com/content/n6293v8808n5g836/ this] paper - we also have full text available):
 
  
 
* 'Homogenize' (mush) approx 40 mg pea with a pestle in 300ug of 5% chelex solution for 1 min   
 
* 'Homogenize' (mush) approx 40 mg pea with a pestle in 300ug of 5% chelex solution for 1 min   
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* 100ml of agarose: 1 grams of agarose powder to 100ml of 1% TBE solution
 
* 100ml of agarose: 1 grams of agarose powder to 100ml of 1% TBE solution
* Microwaved the agarose, cooled to 50 degrees, added 10ul of ethidium bromide stock solution
+
* Microwaved the agarose, cooled to 50 degrees, added 5ul of ethidium bromide stock solution
 +
* Poured agarose into mould and waited to cool
 +
* Ladder = far, template = close
 +
* Electrophoresed - started at 80V, settled at around 130V
 +
 
 +
== 2nd attempt ==
 +
 
 +
* Blend peas with salt and detergent according to [http://learn.genetics.utah.edu/content/labs/extraction/howto/ this] protocol. Sieve.
 +
* Incubate for 15 mins at 60°C (optional step that we didn't take)
 +
* Centrifuge - recover supernatant
 +
* Add proteinease K (100 ul of 1mg / ml solution to 300 ul of pea template) - incubate for 1 hr at 50C (action of proteinase k) then 94 C for 10 mins (inactivation of proteinase K)
 +
* Precipitation to follow

Revision as of 21:37, 18 July 2012

We are using primers for plants to test and refine our DNA extraction / PCR technique. First project is to test for peas. Inspiration and primers are in this paper.

1st attempt - 17 and 18/7/12

Extraction (From this paper - we also have full text available):

  • 'Homogenize' (mush) approx 40 mg pea with a pestle in 300ug of 5% chelex solution for 1 min
  • Vortex for 10s then boil for 5 mins, then vortex again for 10s. (Hot plate lost heat in the middle so we boiled for 8 mins)
  • Centrifuge for 1 min - recover supernatant and use as template

PCR:

  • Prepare sample with 12.5 ul of Taq ready mix, 2 ul of each primer, 3 ul of template, and 5.5 ul of distilled water.
  • Denature at 96°C for 5 mins
  • 40 cycles of D = 96°C for one minute, A = 58°C for 30 seconds, E = 72°C for one minute.
  • Put paraffin on top after 5 mins (should have been before start)

Electrophoresis:

Quantities of chemicals:

  • 1% TBE, 1 part "TBE 10x" to 9 parts water
  • Agarose, 1 gram per 100ml of TBE
  • Ethidium bromide stock solution, 1 gram of powdered EtBr per 100ml of TBE
  • 2ul of ethidium bromide stock solution per 40ml of agarose

Protocol:

  • 100ml of agarose: 1 grams of agarose powder to 100ml of 1% TBE solution
  • Microwaved the agarose, cooled to 50 degrees, added 5ul of ethidium bromide stock solution
  • Poured agarose into mould and waited to cool
  • Ladder = far, template = close
  • Electrophoresed - started at 80V, settled at around 130V

2nd attempt

  • Blend peas with salt and detergent according to this protocol. Sieve.
  • Incubate for 15 mins at 60°C (optional step that we didn't take)
  • Centrifuge - recover supernatant
  • Add proteinease K (100 ul of 1mg / ml solution to 300 ul of pea template) - incubate for 1 hr at 50C (action of proteinase k) then 94 C for 10 mins (inactivation of proteinase K)
  • Precipitation to follow