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"| | |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]] }}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}} | ||
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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 | ||
* | * 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. CDKN2A, | 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: PcTF vs. PcTF mock
1. Name: CDKN2A, chr9
2. Name: MMP12, chr 11
3. Name: NPPA, chr 1
4. Name: EOMES, chr 3
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