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 analysis: bird's eye view of H3K27me3 enrichment | ||
---- | ---- | ||
'''H3K27me3 enrichment'''<br> | '''H3K27me3 enrichment'''<br> | ||
* Completed H3K27me3 (lane | * Completed H3K27me3 (lane 6) "BAM --> assembly" workflow | ||
* Open in SeqMan pro to explore known silenced vs. active genes | * Open in SeqMan pro to explore known silenced vs. active genes | ||
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Based on Carly's control gene list [http://openwetware.org/wiki/Haynes_Lab:Notebook/Synthetic_Biology_and_Bioinformatics_for_Predictable_Control_of_Therapeutic_Genes/2012/05/28]; CDKN2A and MMP12 added by me<br><br> | |||
{| {{table}} | {| {{table}} | ||
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| Gene || Chromosome || Expected state || Observed max. DOC* | | Gene || Chromosome || Expected state || Observed max. DOC* | ||
|- | |- | ||
| CDKN2A || chr9 || silent (H3K27me3+) || | | ALAS1 || chr 3 || active || ~160 | ||
| MMP12 || chr11 || silent (H3K27me3+) || --- | |- | ||
| 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 || ~130 | |||
|- | |||
| HPRT1 || chr X (24) || active || ~150 | |||
|- | |||
| PGK1 || chr X (24) || active || ~240 | |||
|- | |||
| CDKN2A || chr9 || silent (H3K27me3+) || ~90 | |||
|- | |||
| MMP12 || chr11 || silent (H3K27me3+) || ~18 | |||
|- | |||
| MYT1 || chr20 || silent (H3K27me3+) || '''~270''' | |||
|- | |||
| OLIG1 || chr21 || silent (H3K27me3+) || 0 | |||
|- | |||
| OLIG2 || chr21 || silent (H3K27me3+) || ~130 | |||
|} | |} | ||
Revision as of 18:07, 6 January 2013
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01/05/13
H3K27me3 enrichment
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