Team:Vanderbilt/Notebook

From 2014.igem.org

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<div style="color:black;font-size:11pt">'''March 27th'''</div>
<div style="color:black;font-size:11pt">'''March 27th'''</div>
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* Extracted genomic DNA from 100 mg of <i>Arabidopsis thalina </i> leaves using a Viogene DNA extraction kit. Samples were labeled ZIN for zingiberene.
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* Extracted genomic DNA from 100 mg of <i>Arabidopsis thaliana </i> leaves using a Viogene DNA extraction kit. Samples were labeled ZIN for zingiberene.
* Two samples were prepared and nanodropped. The concentration of the first was 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA.  
* Two samples were prepared and nanodropped. The concentration of the first was 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA.  
<div style="color:black;font-size:11pt">'''March 30th'''</div>
<div style="color:black;font-size:11pt">'''March 30th'''</div>
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* ZIN1, ZIN2, CAR1, and CAR2 all show a faint but distinct DNA band above the highest rung on the DNA ladder (>10kb), showing the presence of DNA. No bands were seen on the kit flow-through. Indicates successful genomic extraction.  
* ZIN1, ZIN2, CAR1, and CAR2 all show a faint but distinct DNA band above the highest rung on the DNA ladder (>10kb), showing the presence of DNA. No bands were seen on the kit flow-through. Indicates successful genomic extraction.  
*Preformed a second genomic extraction on <i>Picea abies </i> to improve yield. Nanodrop shows CAR3 to be at 6.2 ng/ul and CAR4 to be 11.5 ng/ul.
*Preformed a second genomic extraction on <i>Picea abies </i> to improve yield. Nanodrop shows CAR3 to be at 6.2 ng/ul and CAR4 to be 11.5 ng/ul.
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* Extracted genomic DNA from <i> Gossypim hirsutum </i>. Samples nanodroppped: CAD1 1.8 ng/ul and CAD2 7.8 ng/ul.  
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* Extracted genomic DNA from <i> Gossypium hirsutum </i>. Samples nanodroppped: CAD1 1.8 ng/ul and CAD2 7.8 ng/ul.  
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<div style="color:black;font-size:11pt">'''April 2nd'''</div>
<div style="color:black;font-size:11pt">'''April 2nd'''</div>
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* Extracted genomic DNA from <i> Salvia Officinalis </i>. Samples nanodropped: SAB1 7.5 ng/ul, and SAB 11.4 ng/ul.
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* Extracted genomic DNA from <i> Salvia officinalis </i>. Samples nanodropped: SAB1 7.5 ng/ul, and SAB 11.4 ng/ul.
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* Extracted genomic DNA from <i> Mentha cintrata </i>. Samples nanodropped: LNR1 3.4 ng/ul, LNR2 6.2 ng/ul, LNR3 7.3 ng/ul
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* Extracted genomic DNA from <i> Mentha citrata </i>. Samples nanodropped: LNR1 3.4 ng/ul, LNR2 6.2 ng/ul, LNR3 7.3 ng/ul
* E. coli containing p404GALS and pDZ207 from Addgene were grown on LB plates with ampicilin. These were miniprepped using a Viogen kit. Samples nanodropped: p404GALS (A) 130.2 ng/ul, p404GALS (B) 112.3 ng/ul, pDZ207 (A) 145.3 ng/ul, pDZ207 (B) 84.1 ng/ul.  
* E. coli containing p404GALS and pDZ207 from Addgene were grown on LB plates with ampicilin. These were miniprepped using a Viogen kit. Samples nanodropped: p404GALS (A) 130.2 ng/ul, p404GALS (B) 112.3 ng/ul, pDZ207 (A) 145.3 ng/ul, pDZ207 (B) 84.1 ng/ul.  
<div style="color:black;font-size:11pt">'''April 3rd'''</div>
<div style="color:black;font-size:11pt">'''April 3rd'''</div>
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* Extracted genomic DNA again from <i> Arabadopsis thalina </i>. Sample nanodropped: LNS1 53.4 ng/ul, LNS2 585.2 ng/ul
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* Extracted genomic DNA again from <i> Arabidopsis thaliana </i>. Sample nanodropped: LNS1 53.4 ng/ul, LNS2 585.2 ng/ul
* Ran gel on LNR1, LNR2, LNR3, LNS1, LNS2, SAB1, and SAB2. All show high weight DNA bands, with Linalool (S) samples having the brightest.
* Ran gel on LNR1, LNR2, LNR3, LNS1, LNS2, SAB1, and SAB2. All show high weight DNA bands, with Linalool (S) samples having the brightest.

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Lab Notebook



Spring 2014

March 27th
  • Extracted genomic DNA from 100 mg of Arabidopsis thaliana leaves using a Viogene DNA extraction kit. Samples were labeled ZIN for zingiberene.
  • Two samples were prepared and nanodropped. The concentration of the first was 2.6 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA.
March 30th
  • Extracted genomic DNA from 100 mg of Picea abies needles using the same extraction kit and protocol. Samples were labeled CAR for carene.
  • Two samples were prepared and nanodropped. The concentration of the first was 0.9 ng/ul, and the second was 3.5 ng/ul of DNA, indicating a minimal yield of DNA.
March 31th
  • Ran a 0.6 % argarose gel on the DNA extracted from ZIN and CAR, as well as the column flow-through from the kit.
  • ZIN1, ZIN2, CAR1, and CAR2 all show a faint but distinct DNA band above the highest rung on the DNA ladder (>10kb), showing the presence of DNA. No bands were seen on the kit flow-through. Indicates successful genomic extraction.
  • Preformed a second genomic extraction on Picea abies to improve yield. Nanodrop shows CAR3 to be at 6.2 ng/ul and CAR4 to be 11.5 ng/ul.
  • Extracted genomic DNA from Gossypium hirsutum . Samples nanodroppped: CAD1 1.8 ng/ul and CAD2 7.8 ng/ul.

An example of a gel showing high molecular weight (>10 kb) bands corresponding to successfully extracted plant Genomic DNA (in this case, samples LNS1 and LNS2 from Aradopsis DNA)

April 1st
  • Ran a gel on CAR3, CAR4, CAD1, and CAD2. Brighter genomic DNA bands were seen on the cadinene camples than before, but cadinene samples showed significant smearing near the top of the gel.
April 2nd
  • Extracted genomic DNA from Salvia officinalis . Samples nanodropped: SAB1 7.5 ng/ul, and SAB 11.4 ng/ul.
  • Extracted genomic DNA from Mentha citrata . Samples nanodropped: LNR1 3.4 ng/ul, LNR2 6.2 ng/ul, LNR3 7.3 ng/ul
  • E. coli containing p404GALS and pDZ207 from Addgene were grown on LB plates with ampicilin. These were miniprepped using a Viogen kit. Samples nanodropped: p404GALS (A) 130.2 ng/ul, p404GALS (B) 112.3 ng/ul, pDZ207 (A) 145.3 ng/ul, pDZ207 (B) 84.1 ng/ul.
April 3rd
  • Extracted genomic DNA again from Arabidopsis thaliana . Sample nanodropped: LNS1 53.4 ng/ul, LNS2 585.2 ng/ul
  • Ran gel on LNR1, LNR2, LNR3, LNS1, LNS2, SAB1, and SAB2. All show high weight DNA bands, with Linalool (S) samples having the brightest.


April 4th
  • Extracted genomic DNA from Zingiber zermbet . Sample nanodropped: HUM1 31.9 ng/ul and HUM2 18.6 ng/ul
  • Extracted genomic DNA from Ocimum basilicum . Sample nanodropped: GER1 2.3 ng/ul
April 5th
  • Extracted genomic DNA from Santalum album seeds since the sapling was still not fully grown. Sample nanodropped: SAN1 53.8 ng/ul and SAN2 28.4 ng/ul
April 7th
  • Extracted genomic DNA from Perilla frutescens . Sample nanodropped: MYR1 632.8 ng/ul and MYR2 958.6 ng/ul
  • Ran gel on MYR1, MYR2, SAN1, and SAN2. Myrcene samples show bright band at high weight as well as smearing toward bottom. Santelene samples have visible but much fainter genomic DNA band.
April 25th
  • Took 1.8 ul of HUM1 genomic DNA and preformed a PCR with humelene synthase primers.
  • Ran gel on PCR product. Resulted in three total bands, one faint around 1.2 kb, and two bands very close in size just under 3.0 kb.
  • Both ~3 kb bands were gel extracted, combining across all four lanes. Samples nanodropped: HUM-top 8.5 ng/ul, HUM-bottom 10.6 ng/ul.


Summer 2014

August 24th
  • Put text here


Fall 2014

August 24th
  • Put text here
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