User:Karmella Haynes/Notebook/PcTF Genomics/2012/12/26: Difference between revisions
From OpenWetWare
(5 intermediate revisions by the same user not shown) | |||
Line 16: | Line 16: | ||
* 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 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<br><br> | |||
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'' | |||
Revision as of 16:12, 27 December 2012
Pc-TF Genomics | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
12/26/12
ChIP: PcTF vs. PcTF mock
1. Name: CDKN2A, Coordinates: chr9: 21,967,751..21,975,132
2. Name: MMP12, Coordinates: chr11: 102,733,464..102,745,764
3. Name: NPPA, Coordinates: chr1: 11,905,967..11,907,840
4. Name: EOMES, Coordinates: chr3: 27,757,886..27,763,785
|