Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

Dong-Sung Lee†, Chongyuan Luo†, Jingtian Zhou†, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, Conor Fitzpatrick, Carolyn O’Connor, Jesse R. Dixon* & Joseph R. Ecker*
† Co-first author, * Corresponding author

HiGlass Displays

Welcome to our site for browsing human brain 3D genome and DNA methylation data generated in our paper,
“Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.” We have the data available for browsing using an instance of the HiGlass 3D genome browser. Below we have an example dataset that by default loads 3D genome structure and DNA methylation data near the SOX2 gene in astrocytes (left) and layer 2/3 excitatory neurons (right). The center heat maps show the contact frequencies determined by our snm3C-seq experiments from human prefrontal cortex (BA10). The green and purple tracks show CpG (green) and non-CpG (purple) methylation over the corresponding regions. Feel free to move the displayed region of the genome by clicking and dragging or zooming in and out (just like you are using Google maps). You can also search for 3D structure or DNA methylation near your favorite gene by clicking the “gear” icon in the upper right hand corner of the display and choosing “Toggle position search box” and typing in the name of your gene of interest. For more detailed instructions on using HiGlass, please see the HiGlass documentation.

Below we have an instance that displays data from all 14 cell types identified by clustering in our manuscript. When displayed with all 14 cell types at once, the window for each cell is quite small, so feel free to close any unnecessary windows by cliking the “X” in the upper right hand corner. In terms of the cell types listed, we use the following abbreviations (in order by row from left to right): Astro – astrocytes; Endo – endothelial cells; L2_3 – layer 2/3 excitatory neurons; L4 – layer 4 excitatory neurons; L5 – layer 5 excitatory neurons; L6 – layer 6 excitatory neurons; MG – microglia; MP – microglia progenitors; Ndnf – Neuron derived neurotrophic factor (Ndnf)+ inhibitory neurons; ODC – oligodendrocytes; OPC – oligodendrocyte precursor cells; Pvalb – Parvalbumin+ inhibitory neurons; Sst – Somatostatin+ inhibitory neurons; Vip – Vasoactive intestinal polypeptide+ inhibitory neurons.