This repository contains the relevant notebooks used to generate figures in the manuscript:

Emma Kuan, Nicholas Moss, Catalina Sakai et al. Dissecting type I and II interferon impacts on human immune cells in disease by a cell type-specific interferon response atlas, 23 December 2025, PREPRINT (Version 1) available at Research Square

IFN_Fig1.ipynb Experimental design and transcriptomic responses to four different IFNs in 13 immune subsets.

IFN_Fig2.ipynb Transcriptomic features of 13 immune cell subsets in response to IFN-α, IFN-β and IFN-λ1.

IFN_Fig3.ipynb Transcriptomic features of 13 immune cell subsets in responding to IFN-γ and its comparison to IFN-α.

IFN_Fig4.ipynb Dynamics of systemic IFNs and their responses in immune cells in NDMM.

IFN_Fig5.ipynb Application of HIRISA to multiple human immune disease cohorts.

IFN_Sup1.ipynb Differential IFN responses in IFN receptor genes in different immune subsets.

IFN_Sup2.ipynb Comparison of enriched versus PBMC IFN-α response.

IFN_Sup3.ipynb Transcriptomic features of 13 immune cell subsets in response to IFN-α, IFN-β and IFN-λ1

IFN_Sup4.ipynb Transcriptomic features of 13 immune cell subsets in response to IFN-γ.

IFN_Sup5.ipynb IFN-α and IFN-γ scores in NDMM.

IFN_Sup6.ipynb IFN-α and IFN-γ scores in patients with myeloma or infection.

IFN_Score_Generate.R Function to generate donor-level IFN response scores

IFNa_IFNg_Scoring_ISGs_Mat.csv Input ISG response matrix for IFN scoring function