User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/05: Difference between revisions
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* | * ChIP seq analysis: bird's eye view of H3K27me3 enrichment | ||
* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes | |||
---- | ---- | ||
''' | '''H3K27me3 enrichment'''<br> | ||
> | * 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 [http://genome.ucsc.edu/cgi-bin/hgGateway 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<br><br> | |||
{| | {| {{table}} | ||
|- | |- | ||
| | | Gene || Chromosome || Expected state || Observed max. DOC* | ||
|- | |- | ||
| | | CDKN2A || chr9 || silent (H3K27me3+) || --- | ||
| | | MMP12 || chr11 || silent (H3K27me3+) || --- | ||
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|} | |} | ||
Revision as of 16:06, 5 January 2013
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01/05/13
H3K27me3 enrichment
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