User:Karmella Haynes/Notebook/PcTF Genomics

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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


Recent changes

11 September 2014

+ N    17:18 User:Karmella Haynes/Notebook/PcTF Genomics/2014/09/11‎ (2 changes) . . (+1,588) . . (Page history) [Karmella Haynes‎ (2×)]

10 September 2014

+ N    16:00 User:Karmella Haynes/Notebook/PcTF Genomics/2014/09/10‎ (5 changes) . . (+2,450) . . (Page history) [Karmella Haynes‎ (5×)]
       15:28 User:Karmella Haynes/Notebook/PcTF Genomics/2014/09/09 (diff; hist) . .  (+185) . . Karmella Haynes (Talk | contribs) (09/09/14: )
       15:26 User:Karmella Haynes/Notebook/PcTF Genomics (diff; hist) . .  (+50) . . Karmella Haynes (Talk | contribs) (Cell Type Study: )

9 September 2014

       20:09 User:Karmella Haynes/Notebook/PcTF Genomics/2014/09/09 (diff; hist) . .  (+390) . . Karmella Haynes (Talk | contribs) (09/09/14: )


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