User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/05

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  • ChIP seq analysis: bird's eye view of H3K27me3 enrichment
  • ChIP-seq enrichment: PcTF vs. PcTF mock for select genes

H3K27me3 enrichment

  • Completed H3K27me3 (lane 3) "BAM --> assembly" workflow
  • Open in SeqMan pro to explore known silenced vs. active genes


  • Open SeqMan Pro. File > Open > ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
  • In an internet browser, go to the UCSC genome browser. Select Feb. 2009 GRCh37/hg19.
  • Enter a gene name. Click [Submit].
  • Take note of the chromosome number.
  • Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
  • Select Contig > Strategy View to view the enrichment histogram.
  • Select Features > Show Feature Table. Find the gene name. Click on it and the strategy view window will jump to that gene.
  • Click the gene symbol. Zoom in. Tak emote of the maximum depth of coverage (max. DOC).

From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment

Gene Chromosome Expected state Observed max. DOC*
CDKN2A chr9 silent (H3K27me3+) ---
MMP12 chr11 silent (H3K27me3+) ---