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01/05/13
- ChIP seq analysis: bird's eye view of H3K27me3 enrichment
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
| Gene | Chromosome | Expected state | Observed max. DOC*
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| ALAS1 | chr 3 | active | ~160
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| TBP | chr 6 | active | ~160
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| ACTB | chr 7 | active | ~180
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| GUSB | chr 7 | active | ~160
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| PPIA | chr 7 | active | ~90
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| GAPDH | chr 12 | active | ~90
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| B2M | chr 15 | active | 0
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| G6PD | chr X | active | ~130
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| HPRT1 | chr X (24) | active | ~150
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| PGK1 | chr X (24) | active | ~240
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| CDKN2A | chr9 | silent (H3K27me3+) | ~90
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| MMP12 | chr11 | silent (H3K27me3+) | ~18
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| MYT1 | chr20 | silent (H3K27me3+) | ~270
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| OLIG1 | chr21 | silent (H3K27me3+) | 0
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| OLIG2 | chr21 | silent (H3K27me3+) | ~130
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Pc-TF Genomics
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