User:Karmella Haynes/Notebook/PcTF Genomics

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Illumina ChIP-seq

  • General Computing
  • ChIP DNA prep for Illumina:
  • 05/16/12 Fasta --> BAM files: Mark Teng from the Dinu lab (TGEN)
  • Enrichment analysis (DNASTAR software)
    • 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


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