Haynes Lab:Notebook/David Barclay Undergrad Training/Plasmid Transformation/2013/10/27

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(Autocreate 2013/10/27 Entry for Haynes_Lab:Notebook/David_Barclay_Undergrad_Training/Plasmid_Transformation)
Current revision (02:13, 15 November 2013) (view source)
 
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=UPLassay=
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*This is a test run for RT-PCR training. Using gene targets identified in prior research to pancreas differentiation gene sequences.
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==Reaction List==
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{| class="wikitable" style="width: 800px;"
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|- valign="top"
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| '''REACTION LIST'''
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{| width=300px
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|-
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| &nbsp; || '''Template cDNA''' || '''Gene Target'''
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|-
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| Rxn 1: || treated cells || PDX1
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|-
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| Rxn 2: || treated cells || MAFA
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|-
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| Rxn 3: || treated cells || GLP1R
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|-
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| Rxn 4: || treated cells || PCSK1
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|-
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| Rxn 5: || treated cells || IAPP
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|-
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| Rxn 6: || treated cells || KCNQ2
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|-
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| Rxn 7: || treated cells || GAPD (reference gene)
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|-
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| Rxn 8: || untreated cells || PDX1
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|-
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| Rxn 9: || untreated cells || MAFA
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|-
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| Rxn 10: || untreated cells || GLP1R
 +
|-
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| Rxn 11: || untreated cells || PCSK1
 +
|-
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| Rxn 12: || untreated cells || IAPP
 +
|-
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| Rxn 13: || untreated cells || KCNQ2
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|-
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| Rxn 14: || untreated cells || GAPD (reference gene)
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|-
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| Rxn 15: || no template || PDX1
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|-
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| Rxn 16: || no template || MAFA
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|-
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| Rxn 17: || no template || GLP1R
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|-
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| Rxn 18: || no template || PCSK1
 +
|-
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| Rxn 19: || no template || IAPP
 +
|-
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| Rxn 20: || no template || KCN2Q
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|-
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| Rxn 21: || no template || GAPD (reference gene)
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|}
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*Run 3 Each
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*45 Reactions Run
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*Using Variation 2
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Variation 2<br> [[Image:Haynes_UPL_fig2.png|300px|Figure 1]]
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*Using as Reference, discount gene names on left side
-
 
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==Primers==
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*Created from Roche Applied Science https://www.roche-applied-science.com/shop/CategoryDisplay?catalogId=10001&tab=&identifier=Universal+Probe+Library&langId=-1#tab-3
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{| class="wikitable" style="width: 800px;"
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|- valign="top"
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| '''PRIMERS LIST'''
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{| width= 700px
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|-
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| &nbsp; || '''Roche Name''' || '''Left Primer''' || '''Right Primer''' || '''UPL probe'''
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|-
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| PDX1 || NM_000209.3 || aagctcacgcgtggaaag || gccgtgagatgtacttgttgaa || #78, cat.no. 04689011001
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|-
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| MAFA || NM_201589.3 || agcgagaagtgccaactcc || ttgtacaggtcccgctcttt || #39, cat.no. 04687973001
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|-
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| GLP1R || NM_002062.3 || gtggcggccaattactactg || ggccagcagtgtgtacagg || #22, cat.no. 04686969001
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|-
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| PCSK1 || NM_000439.4 || caagagcttgtgaaggacaaga || tctttcagccaagagcacag ||  #1, cat.no. 04684974001
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|-
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| IAPP || NM_000415.2 || ttaccaaattgtagaggctttcg || ccctgcctctatacactcactacc  ||  #77, cat.no. 04689003001
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|-
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| KCNQ2(4) || NM_172108.3 || gacgtcatcgagcagtactca || cccacgatctggtccact || #56, cat.no. 04688538001
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|-
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| GAPD (Ref) || NM_002046.3 || agccacatcgctcagacac || gcccaatacgaccaaatcc || #60, cat.no. 04688589001
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|}
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|}
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__NOTOC__
__NOTOC__

Current revision

Haynes BioBrick Cloning Main project page
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UPLassay

  • This is a test run for RT-PCR training. Using gene targets identified in prior research to pancreas differentiation gene sequences.

Reaction List

REACTION LIST
  Template cDNA Gene Target
Rxn 1: treated cells PDX1
Rxn 2: treated cells MAFA
Rxn 3: treated cells GLP1R
Rxn 4: treated cells PCSK1
Rxn 5: treated cells IAPP
Rxn 6: treated cells KCNQ2
Rxn 7: treated cells GAPD (reference gene)
Rxn 8: untreated cells PDX1
Rxn 9: untreated cells MAFA
Rxn 10: untreated cells GLP1R
Rxn 11: untreated cells PCSK1
Rxn 12: untreated cells IAPP
Rxn 13: untreated cells KCNQ2
Rxn 14: untreated cells GAPD (reference gene)
Rxn 15: no template PDX1
Rxn 16: no template MAFA
Rxn 17: no template GLP1R
Rxn 18: no template PCSK1
Rxn 19: no template IAPP
Rxn 20: no template KCN2Q
Rxn 21: no template GAPD (reference gene)
  • Run 3 Each
  • 45 Reactions Run
  • Using Variation 2

Variation 2
Figure 1

  • Using as Reference, discount gene names on left side

Primers

PRIMERS LIST
  Roche Name Left Primer Right Primer UPL probe
PDX1 NM_000209.3 aagctcacgcgtggaaag gccgtgagatgtacttgttgaa #78, cat.no. 04689011001
MAFA NM_201589.3 agcgagaagtgccaactcc ttgtacaggtcccgctcttt #39, cat.no. 04687973001
GLP1R NM_002062.3 gtggcggccaattactactg ggccagcagtgtgtacagg #22, cat.no. 04686969001
PCSK1 NM_000439.4 caagagcttgtgaaggacaaga tctttcagccaagagcacag #1, cat.no. 04684974001
IAPP NM_000415.2 ttaccaaattgtagaggctttcg ccctgcctctatacactcactacc #77, cat.no. 04689003001
KCNQ2(4) NM_172108.3 gacgtcatcgagcagtactca cccacgatctggtccact #56, cat.no. 04688538001
GAPD (Ref) NM_002046.3 agccacatcgctcagacac gcccaatacgaccaaatcc #60, cat.no. 04688589001


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