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

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 6) "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