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Data

Multiome

v1 (44 samples)

First analysis version. Prototype of all downstream steps.

Samples: 44 total
Conditions: control (no DM060), 3-cyt, IFNg, palmitate, dex (3 samples), Ex-4_HG
Preprocessing: CellRanger-ARC + YAP
Spec: IGVF Beta Cell Networks File Specs
Cluster (code + results):
- igvf-data/igvf_sc-islet_10X-Multiome/scratch/2026_01_30 — sample QC, integration, peak analysis, joint analysis, ChromBPNet
- igvf-data/igvf_sc-islet_10X-Multiome/scratch/2026_02_02 — refined peak calling, differential analysis, ChromBPNet, upload prep
GCP: gs://2025_01_06 (project: igvf-browser-tracks)

v2 (54 samples)

Added 10 samples and refined analysis steps. Current as of 03/21/2026.

Samples: 54 total
Conditions: control (DM060 included), 3-cyt, IFNg, palmitate, dex (all samples), Ex-4_HG
Preprocessing: CellRanger-ARC + YAP
Cluster (code): igvf-data/igvf_sc-islet_10X-Multiome/bin/
Cluster (results): igvf-data/igvf_sc-islet_10X-Multiome/results/
GCP: gs://igvf-data/igvf_sc-islet_10X-Multiome/ (project: beta-cell-networks / vocal-lead-490915-t9)
Schema: SCHEMA.md

v3 (planned)

Reprocess with IGVF single-cell uniform pipeline and repeat downstream analysis.

snm3C-seq

Coming soon