sebepedroslab/early-metazoa-3d-chromatin

Code to reproduce analyses in Kim et al. 2024

early-metazoa-3D-chromatin

Code to reproduce analyses in Kim et al. 2024

Analyses

• Micro-C processing pipeline covering the steps from raw sequenced reads to normalized contact matrices is deposited here. The pipeline is adapted from the 4DN HiC processing pipeline.
• Genome compartment analysis.
• Insulation analysis.
• Identification and annotaiton of chromatin loops.

Data availability

• Raw and processed files are available in GEO repository under accession number GSE260572.
• All public datasets used in this study are listed here.
• Genomes, gene annotations and transposon annotations are deposited in the data folder.
• Identified insulation boundaries, genome compartments and chromatin loops are in the data folder.

Data exploration

Generated datasets could be explored in interactive genome browsers configured for each species: Cowc_GBrowser for Capsaspora owczarzaki
Emue_GBrowser for Ephydatia muelleri
Mlei_GBrowser for Mnemiopsis leidyi
Tadh_GBrowser for Trichoplax adhaerens