Copy-scAT: An R package to infer focal and large-scale copy number alterations using scATAC-seq data
You can find our preprint here.
And you can find instructions and a tutorial for Copy-scAT on GitHub.
3D GENOME ARCHITECTURE
In the paper by Johnston et al (2019), we have generated sub-5 kbp resolution 3D genome maps of patient-derived GBM stem cells. This high resolution allows visualization of individual chromatin loops and enabled us to look at precise regulation of gene expression. In addition, we have generated ChIP-seq data for the looping factor CTCF and for the active enhancer/open chromatin histone mark H3K27ac. Integration of these data allows inference of enhancer/superenhancer gene interactions.
You can use this link to access and download processed 3D genome data, CTCF ChIP-seq and H3K27ac datasets.
ChIP-seq data can also be accessed at the GEO, accession number GSE121601.
You can also visualize 3D genome information (loops, domains and compartments), together with CTCF sites, H3K27ac peaks and super enhancer calls on the WashU Epigenome Browser using this link.
Unprocessed Hi-C data can be requested through the EGA and are available at the following link.
LINKED-READ WHOLE GENOME SEQUENCING OF PEDIATRIC HIGH-GRADE GLIOMAS