These kind of analyses appear to be complicated. Your best bets are a HiC analysis is mouse cortex (http://www.ncbi.nlm.nih.gov/pubmed/22495300) and a 5C analysis on the HoxA cluster in mouse limbs (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873244/).
We have used 4C-seq on many tissues, which seems to be more resistant to problems associated with tissue processing. See for examples http://duboule-lab.epfl.ch/publications
Here are 2 papers worth looking at: J Zhang et al (2012) ChIA-PET analysis of transcriptional chromatin interactions, METHODS 58(3), 289-299 and G Li et al (2010) ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing, GENOME BIOLOGY 11(2), article R22. Good luck.
Dear Daan and Michael,
Thank you for the answers. I think it may be difficult to perform these assays in tissue samples, especially tumor tissues.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology