1. HADACA3 Reference profiles

The organizers provide cell population reference profiles for PDAC (pancreatic cancer). Three reference datasets are available: bulk RNAseq of isolated cell populations, bulk methylation profiles of isolated cell populations and single-cell RNAseq. All references are using publicly available data. Each reference type contains 5 cell types: immune cells (immune), fibroblasts (fibro), endothelial cells (endo), and classical (classic) and basal-like (basal) tumor cells.

– bulk RNAseq cell populations: immune cells and fibroblasts transcriptomic profiles were retrieved from the GTEx Analysis V10 (GTEx portal, link to paper 1 2), endothelial cell transcriptomic profiles were retrieved from GEO GSE135123 (link to paper). Basal-like and classical tumor cell transcriptomic profiles were retrieved from this paper. Preprocess: this reference data has been normalized using edgeR.

– bulk methylation profiles of cell populations: Immune and fibroblasts methylation profiles cells were retrieved from [link to paper](from https://doi.org/10.1186/s12859-021-04381-4). Endothelial cell methylation profiles were retrieved from GSE82234, link to paper. Basal-like and classical cells methylation profiles were retrieved from this paper. Preprocess: this reference dataset consists of aggregated beta value profiles without specific batch effect correction.

– single-cell RNAseq: 3 datasets were retrieved. For Peng et al. the 5 cell types are present (link to paper and download). For Baron et al. only endothelial, immune and fibroblast population are present (link to paper and download). For Raghavan et al, basal-like, classical, endothelial and immune cell populations are present (link to <a href="https://www.cell.com/cell/fulltext/S0092-8674(21)01332-5?_returnURL=htt