User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26: Difference between revisions
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* | * ChIP-seq enrichment: PcTF vs. PcTF mock for select genes | ||
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''' | '''ChIP: PcTF vs. PcTF mock'''<br> | ||
> | * 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 [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'' | |||
Revision as of 15:25, 5 January 2013
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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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