Difference between revisions of "User:Karmella Haynes/Notebook/PcTF Genomics/2013/01/05"

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span>
 
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Pc-TF Genomics</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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|style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
 
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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
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* 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>
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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}}
 
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| Gene || Chromosome || Expected state || Observed max. DOC*
 
| Gene || Chromosome || Expected state || Observed max. DOC*
 
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|-
| CDKN2A || chr9 || silent (H3K27me3+) || ---
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| ALAS1 || chr 3 || active || ~160
 
|-
 
|-
| MMP12 || chr11 || silent (H3K27me3+) || ---
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| TBP || chr 6 || active || ~160
 +
|-
 +
| ACTB || chr 7 || active || ~180
 +
|-
 +
| GUSB || chr 7 || active || ~160
 +
|-
 +
| 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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|-
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| G6PD || chr X || active || ~130
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|-
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| HPRT1 || chr X (24) || active || ~150
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|-
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| PGK1 ||  chr X (24) || active || ~240
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|-
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| CDKN2A || chr9 || silent (H3K27me3+) || ~90
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|-
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| MMP12 || chr11 || silent (H3K27me3+) || ~18
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|-
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| MYT1 || chr20 || silent (H3K27me3+) || '''~270'''
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|-
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| OLIG1 || chr21 || silent (H3K27me3+) || 0
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|-
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| OLIG2 || chr21 || silent (H3K27me3+) || ~130
 
|}
 
|}
  

Latest revision as of 22:20, 26 September 2017

Owwnotebook icon.pngPc-TF Genomics Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png


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