Integrative analysis: igvf Multiome × Augsornworawat2023 Multiome

[adamklie]

Context

Both are multiome datasets of SC-islet samples. Compare igvf-data/igvf_sc-islet_10X-Multiome with public-data/Augsornworawat2023_sc-islet_10X-Multiome.

Tasks

• Integrate RNA into a joint UMAP
• Train ChromBPNet models on ATAC for matched cell types and compare sequence determinants
• Compare peak-to-gene links called in the two datasets (same method)

[adamklie]

Dependencies

• Blocked by Retrain ChromBPNet models at different resolutions #1 (needs ChromBPNet models for comparison), Recall peak-to-gene links using Gaulton lab pipeline #2 (needs peak-to-gene links for comparison)

[adamklie]

Notes from project reorganization (2026-03-23)

Cross-dataset comparison plans filed in manuscripts/beta_cell_networks/bin/comparisons_across_datasets.md. Covers Augsornworawat SC-islet comparison, treated islets, and snm3c vs 10x multiome analyses.

Sub-analyses planned:

• EC subpopulation annotation comparison across assays
• Peak set comparison between primary and SC-islet
• Figure 8: Alignment of SC.beta cell responses to primary islet responses
• Correlation analyses (RNA↔ATAC, RNA↔mCG, mCG↔ATAC, 3C↔RNA at genes)