User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26: Difference between revisions
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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. | * 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]. | * Enter a gene name. Click [Submit]. | ||
* Take note of the chromosome number | * 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. | * 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 ''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 | |||
1. Name: CDKN2A, | From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment<br><br> | ||
1. Name: CDKN2A, chr9 | |||
* SeqMan Pro template ''NC000009(1>141215022) NC_000009'' | * 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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