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. | ||
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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 | ||
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| + | 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'' | ||
Current revision
 Pc-TF Genomics
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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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