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


* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes


----
----
'''H3K27me3 enrichment'''<br>
'''H3K27me3 enrichment'''<br>
* Completed H3K27me3 (lane 3) "BAM --> assembly" workflow
* 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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From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>
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

  • 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*
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 ~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




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