Integrative analysis: igvf SC-islet Multiome × primary islet Multiome

[adamklie]

Context

Compare SC-islet (igvf-data/igvf_sc-islet_10X-Multiome) with primary islet (public-data/islet_10X-Multiome) — both treated with different stimuli.

Tasks

• Integrate RNA into a joint UMAP
• Compare stimulus responses at RNA and ATAC level (differential analysis, gene programs, chromatin accessibility)
• Compare peak-to-gene links (same method)
• Compare sequence determinants via ChromBPNet on matched cell types

[adamklie]

Dependencies

• Blocked by Retrain ChromBPNet models at different resolutions #1 (needs ChromBPNet models), Recall peak-to-gene links using Gaulton lab pipeline #2 (needs peak-to-gene links), Finalize DESeq2 pseudobulk methodology for RNA and ATAC #4 (needs finalized differential analysis for comparison)

[adamklie]

Notes from project reorganization (2026-03-23)

See also #9 — cross-dataset comparison plans are in manuscripts/beta_cell_networks/bin/comparisons_across_datasets.md.

[adamklie]

Status Update (2026-04-09)

Still blocked on #1, #2, #4. Deferred for now.