This is the workflowr project associated with our paper "Reorganization of 3D Genome Structure May Contribute to Gene Regulatory Evolution in Primates." The output website of this repo, containing specifics on and figures from the analyses performed in the manuscript (and many more not seen in the manuscript) can be found here.
In this project, we collected Hi-C data (chromosome conformation) from 4 human and 4 chimpanzee induced pluripotent stem cell (iPSC) lines. We also overlaid these data with existing RNA-seq data (gene expression) from the same individuals, previously collected by the Gilad lab, as well as publicly available functional genomic data from human iPSCs and ESCs. Perhaps the most surprising result is relatively low conservation of topologically associating domain (TAD) structures between humans and chimpanzees, which have highly syntenic genomes. We also found intriguing results with chromosome conformation associating with gene expression and functional epigenetic marks. For more information, please see the preprint or the paper.
A workflowr project.