cellxgene-contextlisted

# Integrating CellxGene Census Single-Cell Data with ENCODE Bulk Experiments Bridge bulk ENCODE functional genomics data with cell-type-specific expression from the CellxGene Census, the largest unified single-cell RNA-seq atlas, to resolve cell-type contributions to regulatory element activity. ## Scientific Rationale **The question**: "Which specific cell types within my tissue drive the regulatory signals I see in bulk ENCODE data?" ENCODE provides deeply sequenced bulk functional genomics (ChIP-seq, ATAC-seq, Hi-C) across hundreds of biosamples. But bulk data from a tissue like "pancreas" is a mixture of acinar cells (~80%), duct cells (~10%), endocrine cells (~5%), and others. An H3K27ac peak in bulk pancreas could be driven by any of these cell types. CellxGene Census provides cell-type-resolved expression data from 50M+ single-cell observations across thousands of datasets, enabling deconvolution of bulk ENCODE signals. ### The Bulk-to-Single-Cell Bridge | Bulk ENCODE Signal | Single-Cell Question | CellxGene Answer | |-------------------|---------------------|-----------------| | H3K27ac peak near INS gene in pancreas | Which cell type expresses INS? | Beta cells (>500 TPM), not acinar (<1 TPM) | | ATAC-seq peak in liver near ALB | Is this hepatocyte-specific? | Yes — ALB expressed only in hepatocytes | | Enhancer active in brain cortex | Neurons or glia? | CellxGene resolves excitatory neurons vs. astrocytes vs. oligodendrocytes | | Broad H3K27ac domain in bloo