User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26: Difference between revisions

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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>}}
|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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==mm/dd/yy==
==12/26/12==
<!-- Precede finished items with a checkmark &#x2713; -->
<!-- Precede finished items with a checkmark &#x2713; -->
* Line item 1
* ChIP-seq enrichment: PcTF vs. PcTF mock for select genes


----
----
'''Line item 1'''<br>
'''ChIP: PcTF vs. PcTF mock'''<br>
> Samples
* 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.


{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
|-valign="top"
| <u>Reagent</u> || <u>Volume</u>
|-
| reagent 1 || # μL
|-
| reagent 2 || #
|-
| reagent 3 || #
|-
| reagent 4 || #
|-
| dH<sub>2</sub>O || #
|-
| &nbsp; || # μL
|}


--> Reaction conditions
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. Take a snapshot
 
 
From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br>
 
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''
 




Latest revision as of 22:20, 26 September 2017

Pc-TF Genomics Main project page
Previous entry      Next entry


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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