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 Pc-TF Genomics
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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 and coordinates.
- 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.
- Navigate to the appropriate coordinates.
- Click the gene symbol. Zoom in. Take a snapshot
From the Haynes & Silver JBC 2011 paper, ChIP-seq experiment
1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132
- SeqMan Pro template NC000009(1>141215022) NC_000009
2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764
- SeqMan Pro template NC000011(1>135008327) NC_000011
3. Name: NPPA, Coordinates: chr1: 11,905,967..11,907,840
- SeqMan Pro template NC000001(1>249240538) NC_000001
4. Name: EOMES, Coordinates: chr3: 27,757,886..27,763,785
- SeqMan Pro template NC000003(1>197960493) NC_000003
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Pc-TF Genomics
