Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Genes/2012/01/18: Difference between revisions
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==Preliminary ENCODE | ==Preliminary UCSC Genome Browser at ENCODE Run Through== | ||
* After taking some preliminary screen shots of genes within the HepG2 and BJ cell line that showed H3K27me3 methylation signal around the promoter I discovered that it would take entirely too long to scroll through the cell lines in order to find 1000s of genes with this mark on the promoter. I need to email the UCSC Genome Browser at ENCODE in order to find out how I will create a filter in the database that will provide a list of genes where the promoter site shows a high level of the H3K27me3 histone methylation. I will need it to be able to find the beginning of the gene's promoter on the UCSC Genome Browser and then show about 500bps to the left and 500bps to the right of the promoter . Ultimately, I want to be able to navigate through the genes in this cell line that show a significant enough H3K27me3 signal at the promoter (everything else with a low H3K27me3 signal I do not care about). | * After taking some preliminary screen shots of genes within the HepG2 and BJ cell line that showed H3K27me3 methylation signal around the promoter I discovered that it would take entirely too long to scroll through the cell lines in order to find 1000s of genes with this mark on the promoter. I need to email the UCSC Genome Browser at ENCODE in order to find out how I will create a filter in the database that will provide a list of genes where the promoter site shows a high level of the H3K27me3 histone methylation. I will need it to be able to find the beginning of the gene's promoter on the UCSC Genome Browser and then show about 500bps to the left and 500bps to the right of the promoter . Ultimately, I want to be able to navigate through the genes in this cell line that show a significant enough H3K27me3 signal at the promoter (everything else with a low H3K27me3 signal I do not care about). | ||
* As of now, this is the protocol that needs to be followed | * As of now, this is the protocol that needs to be followed |
Revision as of 02:51, 25 January 2012
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Preliminary UCSC Genome Browser at ENCODE Run Through
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