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
    • K562 sets 1-3, SKNSH sets 1-3, U2OS sets 1-2 (1:1000 cDNA) 5/16/14
    • K562 sets 1-3, SKNSH sets 1-3, U2OS sets 1-2 (1:100 cDNA) 5/16/14
  • Dr. Haynes - lentiviral transduction of PcTF's

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

29 January 2015

+      12:46 User:Karmella Haynes/Notebook/PcTF Genomics/2015/01/28‎ (2 changes) . . (+130) . . (Page history) [Karmella Haynes‎ (2×)]

28 January 2015

+ N    18:34 User:Karmella Haynes/Notebook/PcTF Genomics/2015/01/28‎ (2 changes) . . (+2,412) . . (Page history) [Karmella Haynes‎ (2×)]
  N    18:23 User:Karmella Haynes/Notebook/PcTF Genomics/2015 (diff; hist) . .  (+779) . . Karmella Haynes (Talk | contribs) (Autocreate Year 2015 Entry for User:Karmella_Haynes/Notebook/PcTF_Genomics)
  N    18:23 User:Karmella Haynes/Notebook/PcTF Genomics/2015/01 (diff; hist) . .  (+201) . . Karmella Haynes (Talk | contribs) (Autocreate Month 2015/01 Entry for User:Karmella_Haynes/Notebook/PcTF_Genomics)


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