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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 |
---
|
| HPRT1 |
chr X (24) |
active |
---
|
| PGK1 |
chr X (24) |
active |
---
|
| CDKN2A |
chr9 |
silent (H3K27me3+) |
---
|
| MMP12 |
chr11 |
silent (H3K27me3+) |
---
|
| MYT1 |
chr20 |
silent (H3K27me3+) |
---
|
| OLIG1 |
chr21 |
silent (H3K27me3+) |
---
|
| OLIG2 |
chr21 |
silent (H3K27me3+) |
---
|
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Pc-TF Genomics
