User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26

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==mm/dd/yy==
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==12/26/12==
<!-- Precede finished items with a checkmark &#x2713; -->
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* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes
* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes
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* Open in SeqMan pro to see raw values for four genes from 2011 paper.
* Open in SeqMan pro to see raw values for four genes from 2011 paper.
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1. CDKN2A,
 
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{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
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Workflow
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|-valign="top"
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* Open SeqMan Pro. ''File > Open >'' ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
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| <u>Reagent</u> || <u>Volume</u>  
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* In an internet browser, go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
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|-
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* Enter a gene name. Click [Submit].
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| reagent 1 || # μL
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* Take note of the chromosome number.
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|-
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* Find the appropriate assembly template in the SeqMan Pro (e.g., NC_000001 for chromosome 1). Double click it.
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| reagent 2 || #
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* Select ''Contig > Strategy View'' to view the enrichment histogram.
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|-
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* Select Features > Show Feature Table. Find the gene name. Click on it and the strategy view window will jump to that gene.
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| reagent 3 || #
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* Click the gene symbol. Zoom in. Take a snapshot
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|-
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| reagent 4 || #
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From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>
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| dH<sub>2</sub>O || #
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1. Name: CDKN2A, chr9
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| &nbsp; || # μL
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* SeqMan Pro template ''NC000009(1>141215022) NC_000009''
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|}
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2. Name: MMP12, chr 11
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* SeqMan Pro template ''NC000011(1>135008327) NC_000011''
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3. Name: NPPA, chr 1
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* SeqMan Pro template ''NC000001(1>249240538) NC_000001''
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4. Name: EOMES, chr 3
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* SeqMan Pro template ''NC000003(1>197960493) NC_000003''
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--> Reaction conditions
 

Current revision

Pc-TF Genomics Main project page
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12/26/12

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

ChIP: PcTF vs. PcTF mock

  • Completed PcTF (lane 1) and PcTF mock (lane 2) BAM --> assembly workflow
  • Open in SeqMan pro to see raw values for four genes from 2011 paper.


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. Take a snapshot


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

1. Name: CDKN2A, chr9

  • SeqMan Pro template NC000009(1>141215022) NC_000009

2. Name: MMP12, chr 11

  • SeqMan Pro template NC000011(1>135008327) NC_000011

3. Name: NPPA, chr 1

  • SeqMan Pro template NC000001(1>249240538) NC_000001

4. Name: EOMES, chr 3

  • SeqMan Pro template NC000003(1>197960493) NC_000003




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