Publication

Colli, M.L., Ramos-Rodríguez, M., Nakayasu, E.S. et al. An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells. Nat Commun 11, 2584 (2020). https://doi.org/10.1038/s41467-020-16327-0

Note: As this work is the result of a collaboration and Décio Eizirik’s group was the lead in this project, some results shown here might not exactly coincide with the ones published in the paper, as some analyses were re-run later with modified parameters.

Data availability

The different datasets that were used in the publication can be downloaded from GEO with the following accessions:

GEO ID Experiment Link
GSE133219 ATAC-seq https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133219
GSE133218 RNA-seq https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133218
GSE148058 RNA-seq 2 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148058

Data processing

ATAC-seq

ATAC-seq and ChIP-seq experiments were processed using the custom pipelineNGS R package. The specific scripts used for processing such data can be found at the corresponding folders inside data/IFNa/, in the source code repository for this website.