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

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(Autocreate 2013/01/05 Entry for User:Karmella_Haynes/Notebook/PcTF_Genomics)
 
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==mm/dd/yy==
==01/05/13==
<!-- Precede finished items with a checkmark &#x2713; -->
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* Line item 1
* ChIP seq analysis: bird's eye view of H3K27me3 enrichment
 
* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes


----
----
'''Line item 1'''<br>
'''H3K27me3 enrichment'''<br>
> Samples
* 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>


{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
{| {{table}}
|-valign="top"
| <u>Reagent</u> || <u>Volume</u>
|-
| reagent 1 || # μL
|-
|-
| reagent 2 || #
| Gene || Chromosome || Expected state || Observed max. DOC*
|-
|-
| reagent 3 || #
| CDKN2A || chr9 || silent (H3K27me3+) || ---
|-
| MMP12 || chr11 || silent (H3K27me3+) || ---
| reagent 4 || #
|-
| dH<sub>2</sub>O || #
|-
| &nbsp; || # μL
|}
|}


--> Reaction conditions
 




Revision as of 16:06, 5 January 2013

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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).


From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment

Gene Chromosome Expected state Observed max. DOC*
CDKN2A chr9 silent (H3K27me3+) --- MMP12 chr11 silent (H3K27me3+) ---




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