User:Karmella Haynes/Notebook/PcTF Genomics

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(Illumina ChIP-seq)
(Illumina ChIP-seq)
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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]
** 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]
** Input DNA - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/25 01/25/13]
** Input DNA - [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/25 01/25/13]
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* [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/05/16 05/16/12] Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
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* Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
* Enrichment analysis (DNASTAR software)
* Enrichment analysis (DNASTAR software)
 +
** MACS: BAM --> BED (peaks), done by Mark Teng [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/05/16 05/16/12]
** DNASTAR: BAM --> peaks/ enrichment histograms workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/13 12/13/2012]
** DNASTAR: BAM --> peaks/ enrichment histograms workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/13 12/13/2012]
** DNASTAR: BAM --> wig files for UCSC browser workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/07 01/07/2013]
** DNASTAR: BAM --> wig files for UCSC browser workflow [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2013/01/07 01/07/2013]

Revision as of 15:22, 3 April 2014

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Illumina ChIP-seq

  • General Computing
  • ChIP DNA prep for Illumina:
  • Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
  • Enrichment analysis (DNASTAR software)
    • MACS: BAM --> BED (peaks), done by Mark Teng 05/16/12
    • DNASTAR: BAM --> peaks/ enrichment histograms workflow 12/13/2012
    • DNASTAR: BAM --> wig files for UCSC browser workflow 01/07/2013
    • STAR: Sample BED vs. Input BED --> clean up false positive enrichment and filter out repeat-sequence hits 02/10/2014



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

17 November 2014

+ N    14:53 User:Karmella Haynes/Notebook/PcTF Genomics/2014/11/16‎ (3 changes) . . (+1,486) . . (Page history) [Karmella Haynes‎ (3×)]

15 November 2014

+ N    15:08 User:Karmella Haynes/Notebook/PcTF Genomics/2014/11/15‎ (3 changes) . . (+1,700) . . (Page history) [Karmella Haynes‎ (3×)]

14 November 2014

+ N    16:34 User:Karmella Haynes/Notebook/PcTF Genomics/2014/11/14‎ (3 changes) . . (+1,082) . . (Page history) [Karmella Haynes‎ (3×)]


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