single-cell-encodelisted

# Single-Cell ENCODE Data ## When to Use - User wants to find or analyze single-cell data (scRNA-seq, scATAC-seq, snRNA-seq) from ENCODE - User asks about "single-cell", "scRNA-seq", "scATAC-seq", "cell type annotation", or "single-nucleus" - User needs to integrate ENCODE single-cell data with bulk epigenomic profiles - User wants to identify cell-type-specific regulatory elements from single-cell chromatin accessibility - Example queries: "find scRNA-seq data in ENCODE for brain", "what snATAC-seq is available?", "integrate single-cell with bulk ChIP-seq" Help the user find and work with ENCODE single-cell genomics data, understand quality limitations relative to bulk assays, and integrate single-cell with bulk ENCODE profiles for cell-type-resolved regulatory analysis. ## Literature Foundation | # | Reference | Key Contribution | |---|-----------|-----------------| | 1 | Mawla & Huising 2019, Endocrinology, DOI:10.1210/en.2018-01037 (~200 cit) | Cross-study scRNA-seq meta-analysis revealing that only ~1-2% of heterogeneity-driving genes replicate across studies; TIN-based quality assessment; detection-limit awareness framework. PMC6609986. | | 2 | Regev et al. 2017, eLife, DOI:10.7554/eLife.27041 (~1,200 cit) | Human Cell Atlas white paper defining the vision for comprehensive single-cell reference maps of all human cells. Establishes community standards for cell atlas construction. | | 3 | Stuart et al. 2019, Cell, DOI:10.1016/j.cell.2019.05.031 (~7,000 cit) | Seurat