Evolution of Topologically Associating Domains in Deuterostomes Enabled the Expansion of Cis-Regulatory Interactions and Regulatory Pleiotropy

This repository contains the following: CTCF binding sites: FIMO output for all species in the study. Ciona intestinalis genome: sequence (.fa), chromosome sizes (.chromsizes) and gene annotation (.gff). Saccoglossus kowalevskii genome: sequence (.fa), chromosome sizes (.chromsizes) and gene annotation (.gff). Orthogroups: output from OrthoFinder v2. HiC files (.mcool): all .mcool files used in the study except for the mouse (4D nucleome ID: 4DNESIZMF58U, 4DNESLUJ3INP, 4DNFI5TWFPOL, 4DNFI9BMR5E1). ChIP-seq for Saccoglossus kowalevskii Cross-validation folds for Saccoglossus kowalevskii and Strongylocentrotus purpuratus. Unfiltered ATAC-seq peaks for Saccoglossus kowalevskii, Nematostella vectensis and Strongylocentrotus purpuratus. Raw Stripenn output for all species in the study. Scripts and Robjects (including scRNA-seq and scATAC-seq data) used to produce figures in the study.