For general interaction analysis, TAD identification, and compartment-level studies, we recommend a sequencing depth of 100X, as higher depth directly translates to higher resolution. Based on experience with human and mouse projects, a depth of 150X achieves a resolution of approximately 10 kb, which is sufficient for loop analysis. For other species, or if the research specifically targets loop detection, we recommend increasing the depth to 300X.
Compartment A/B (Euchromatin/Heterochromatin): These represent large-scale spatial segregation of active and inactive chromatin.
TADs (Topologically Associating Domains): These are the primary functional units within compartments, characterized by frequent internal interactions. Their boundaries are highly conserved and typically enriched with CTCF binding sites and active transcription marks.
LADs (Lamina-Associated Domains): These domains exhibit weaker interactions within compartments and consist primarily of transcriptionally silent chromatin, enriched with heterochromatic histone marks such as H3K27me3 and H3K9me3.
Loops (Chromatin Loops): These structures show significantly higher interaction frequencies than surrounding regions within a TAD (e.g., promoter-enhancer interactions). As the most refined level of hierarchical structure, loops operate at the scale of regulatory element binding and individual genes.
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