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

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01/05/13

  • 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


Workflow

  • 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).


Based on Carly's control gene list [1]; CDKN2A and MMP12 added by me

Gene Chromosome Expected state Observed max. DOC*
ALAS1 chr 3 active ~160
TBP chr 6 active ~160
ACTB chr 7 active ~180
GUSB chr 7 active ~160
PPIA chr 7 active ~90
GAPDH chr 12 active ~90
B2M chr 15 active 0
G6PD chr X active ~130
HPRT1 chr X (24) active ~150
PGK1 chr X (24) active ~240
CDKN2A chr9 silent (H3K27me3+) ---
MMP12 chr11 silent (H3K27me3+) ---
MYT1 chr20 silent (H3K27me3+) ---
OLIG1 chr21 silent (H3K27me3+) ---
OLIG2 chr21 silent (H3K27me3+) ---




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