Difference between revisions of "Haynes Lab:Notebook/Synthetic Biology and Bioinformatics for Predictable Control of Therapeutic Gene2"

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==Project Description/Abstract==
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==Phase 3: Expression==
* Since a comprehensive ChIP map is not available for osteosarcoma, I will identify genes associated with H3K27me3 in liver (HepG2) and fibroblast (BJ) cell lines. ChIP is available through the Encyclopedia of DNA Elements (ENCODE) (3). I will extract a list of genes with H3K27me3 near the transcription start site (promoter) as well as genes with a broad distribution of H3K27me3 to determine later on if H3K27me3 localization influences Pc-TF function. I will also determine which CBX isoforms are at each locus to determine variations between H3K27me3 sites.
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At this stage the necessary bioinformatics has been performed in order to identify which genes could be potentially turned on by PcTF. Using Real-Time qRT-PCR we can determine which genes form that list are up-regulated and what further analysis need to be performed. We will also continue research by seeing how cell phenotype and growth are affected by PcTF.
  
 
==Notes==
 
==Notes==
* Phase 1 in progress
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* Phase 3 is in progress
  
  

Revision as of 18:55, 16 April 2013

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Phase 3: Expression

At this stage the necessary bioinformatics has been performed in order to identify which genes could be potentially turned on by PcTF. Using Real-Time qRT-PCR we can determine which genes form that list are up-regulated and what further analysis need to be performed. We will also continue research by seeing how cell phenotype and growth are affected by PcTF.

Notes

  • Phase 3 is in progress


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