Associated manuscript: Aberrant brain-type neuronal programs in large-cell pancreatic neuroendocrine carcinoma
Zenodo DOI: https://doi.org/10.5281/zenodo.20097468
GEO accession: GSE291816
This repository contains the analysis code and notebooks underlying the panNEC atlas. Fresh-frozen tumour tissue from 5 patients with high-grade large-cell pancreatic neuroendocrine carcinoma (panNEC) was profiled by single-nucleus RNA-sequencing (snRNA-seq), yielding 45,015 nuclei across different shared and unique cell states. Single-nucleus transcriptomics revealed two distinct neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation programme, and a stress-responsive state enriched for heat stress, hypoxia, and glycolysis.
Processed data (h5ad) & the list of 4,000 highly variable genes are available via Zenodo. Raw CellRanger count matrices are deposited at GEO (GSE291816).
Dr. Olivia Debnath — olivia_debnath@dfci.harvard.edu
Dr. Hilmar Berger — hilmar.berger@charite.de &
Dr. Naveed Ishaque - naveed.ishaque@bih-charite.de
panNEC_study2025/
├── Figure_1/ # Main figure 1 notebooks
├── Figure_2/ # Main figure 2 notebooks
├── Supplementary_figure_analyses/ # Notebooks per latest manuscript supplementary figure numbering
├── bioarxiv_2025_extended/ # Original bioRxiv extended data figures (archived)
│ ├── Extended_1/
│ ├── Extended_2/
│ ├── Extended_3/
│ └── Extended_4/
├── analysis/ # Core atlas building pipeline
├── snRNAseq_preprocessing/ # Preprocessing pipeline (SoupX, alignment)
└── readme.md