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

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* Completed PcTF (lane 1) and PcTF mock (lane 2) BAM --> assembly workflow
* 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.
* Open in SeqMan pro to see raw values for four genes from 2011 paper.
 +
Workflow
Workflow
-
* Go to the [http://genome.ucsc.edu/cgi-bin/hgGateway UCSC genome browser]. Select Feb. 2009 GRCh37/hg19.
+
* Open SeqMan Pro. ''File > Open >'' ...navigate to the desired ###.assembly file in the SeqMan NGen Projects folder. Processing takes 5 -10 minutes.
-
* Search for the gene by name. Get coordinates
+
* 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 and coordinates.
 +
* 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.
 +
* Navigate to the appropriate coordinates.
 +
* Click the gene symbol. Zoom in. Take a snapshot
 +
 
 +
 
 +
From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>
 +
 
 +
1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132
 +
* SeqMan Pro template ''NC000009(1>141215022) NC_000009''
 +
 
 +
2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764
 +
* SeqMan Pro template ''NC000011(1>135008327) NC_000011''
 +
 
 +
3. Name: NPPA, Coordinates: chr1: 11,905,967..11,907,840
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* SeqMan Pro template ''NC000001(1>249240538) NC_000001''
-
1. CDKN2A,  
+
4. Name: EOMES, Coordinates: chr3: 27,757,886..27,763,785
 +
* SeqMan Pro template ''NC000003(1>197960493) NC_000003''

Revision as of 19:12, 27 December 2012

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 and coordinates.
  • 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.
  • Navigate to the appropriate coordinates.
  • Click the gene symbol. Zoom in. Take a snapshot


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

1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132

  • SeqMan Pro template NC000009(1>141215022) NC_000009

2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764

  • SeqMan Pro template NC000011(1>135008327) NC_000011

3. Name: NPPA, Coordinates: chr1: 11,905,967..11,907,840

  • SeqMan Pro template NC000001(1>249240538) NC_000001

4. Name: EOMES, Coordinates: chr3: 27,757,886..27,763,785

  • SeqMan Pro template NC000003(1>197960493) NC_000003




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