User:Karmella Haynes/Notebook/PcTF Genomics

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(Cell Type Study)
(Cell Type Study)
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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]
** SK-N-SH - TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2012/12/27 12/27/12]
** U2OS TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/01/27 01/27/14]
** U2OS TRIzol prep [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/01/27 01/27/14]
 +
* Dr. Haynes - Quality control mCherry & GAPDH runs
 +
**
==PcTF-Reporter Activation==
==PcTF-Reporter Activation==

Revision as of 17:25, 27 May 2014

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Illumina ChIP-seq

  • General Computing
  • ChIP DNA prep for Illumina:
  • IP samples Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
  • Input sample Fasta --> BAM file: Karthik Velmurugan on 5/16/13 (external hard drive)
  • 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
  • Dr. Haynes - Quality control mCherry & GAPDH runs

PcTF-Reporter Activation

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


Synthetic Repression

  • Gal4-EED/luc staining experiments


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