compare-biosampleslisted

# Compare ENCODE Data Across Biosamples ## When to Use - User wants to compare ENCODE experiments across different tissues, cell lines, or biosamples - User asks about "tissue comparison", "cell-type differences", "tissue-specific enhancers", or "cross-tissue" - User needs to identify constitutive vs tissue-specific regulatory elements - User wants to map data availability across multiple biosamples before integrative analysis - Example queries: "compare H3K27ac between liver and pancreas", "what marks are tissue-specific?", "find constitutive promoters across all tissues" Help the user systematically compare data availability and experiments across different biosamples to identify tissue-specific regulatory patterns, constitutive elements, and cross-tissue differences. ## Scientific Rationale Cross-biosample comparison is the foundation of understanding tissue-specific gene regulation. Regulatory elements -- particularly enhancers -- are the primary drivers of cell-type identity, with promoters being largely shared across tissues. Comparing the same assay across multiple biosamples reveals which regulatory elements are constitutive (shared) versus tissue-specific (unique to one or few cell types). **The core question**: "Which regulatory features distinguish tissue A from tissue B, and which are shared?" This requires careful matching of datasets, awareness of batch effects, and understanding of the biosample hierarchy to avoid confounding biological signal with techn