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

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(Autocreate 2013/01/05 Entry for User:Karmella_Haynes/Notebook/PcTF_Genomics)
 
(01/05/13)
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==mm/dd/yy==
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==01/05/13==
 
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* Line item 1
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* ChIP seq analysis: bird's eye view of H3K27me3 enrichment
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----
 
----
'''Line item 1'''<br>
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'''H3K27me3 enrichment'''<br>
> Samples
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* 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 [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).
 +
 
 +
 
 +
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>
  
{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
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{| {{table}}
|-valign="top"
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|-
| <u>Reagent</u> || <u>Volume</u>
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| Gene || Chromosome || Expected state || Observed max. DOC*
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|-
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| ALAS1 || chr 3 || active || ~160
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|-
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| TBP || chr 6 || active || ~160
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|-
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| ACTB || chr 7 || active || ~180
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|-
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| GUSB || chr 7 || active || ~160
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|-
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| PPIA || chr 7 || active || ~90
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|-
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| GAPDH || chr 12 || active || ~90
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|-
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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
 
|-
 
|-
| reagent 1 || # μL
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| PGK1 || chr X (24) || active || ~240
 
|-
 
|-
| reagent 2 || #
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| CDKN2A || chr9 || silent (H3K27me3+) || ~90
 
|-
 
|-
| reagent 3 || #
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| MMP12 || chr11 || silent (H3K27me3+) || ~18
 
|-
 
|-
| reagent 4 || #
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| MYT1 || chr20 || silent (H3K27me3+) || '''~270'''
 
|-
 
|-
| dH<sub>2</sub>O || #
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| OLIG1 || chr21 || silent (H3K27me3+) || 0
 
|-
 
|-
| &nbsp; || # μL
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| OLIG2 || chr21 || silent (H3K27me3+) || ~130
 
|}
 
|}
  
--> Reaction conditions
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Revision as of 17:07, 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