User:Karmella Haynes/Notebook/PcTF Genomics

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==Illumina ChIP-seq==
==Illumina ChIP-seq==
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* ChIP DNA prep for Illumina: [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/13 12/13/11],  [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/14 12/14/11], [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/19 12/19/11]
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* ChIP DNA prep for Illumina:  
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* Fasta --> BAM files: Mark Teng
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** Experimental samples - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/13 12/13/11],  [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/14 12/14/11], [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/19 12/19/11]
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* Peak finding DNASTAR Array Star [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/01 21/01/12]
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** Input DNA - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/25 01/25/13]
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* Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
* Enrichment analysis (DNASTAR software)
* Enrichment analysis (DNASTAR software)
** BAM --> peaks/ enrichment histograms workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/13 12/13/2012]
** BAM --> peaks/ enrichment histograms workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/13 12/13/2012]
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** BAM --> wig files for UCSC browser workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/07 01/07/2013]
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<br>
<br>
==Cell Type Study==
==Cell Type Study==
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* Express PcTF (KAH126) in K-562 and SK-N-SH
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* Carly Hom - Express PcTF (KAH126) in K-562 and SK-N-SH
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** K562 - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/18 12/18/12]
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** SK-N-SH - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/27 12/27/12]
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** U2OS TriZOL prep
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==PcTF-Reporter Activation==
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* Measure range of PcTF expression in transiently transfected cells - flow cytometry, [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/06/02 06/02/13]
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==Synthetic Repression==
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* Gal4-EED/luc staining experiments
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Revision as of 19:39, 24 January 2014

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Illumina ChIP-seq

  • ChIP DNA prep for Illumina:
  • Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
  • Enrichment analysis (DNASTAR software)
    • BAM --> peaks/ enrichment histograms workflow 12/13/2012
    • BAM --> wig files for UCSC browser workflow 01/07/2013



Cell Type Study

  • Carly Hom - Express PcTF (KAH126) in K-562 and SK-N-SH

PcTF-Reporter Activation

  • Measure range of PcTF expression in transiently transfected cells - flow cytometry, 06/02/13


Synthetic Repression

  • Gal4-EED/luc staining experiments


Recent changes

18 October 2014

+ N    20:46 User:Karmella Haynes/Notebook/PcTF Genomics/2014/10/18‎ (5 changes) . . (+2,684) . . (Page history) [Karmella Haynes‎ (5×)]


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