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 Pc-TF Genomics
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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).
From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment
| Gene |
Chromosome |
Expected state |
Observed max. DOC*
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| CDKN2A |
chr9 |
silent (H3K27me3+) |
---
|
MMP12 |
chr11 |
silent (H3K27me3+) |
---
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Pc-TF Genomics
