IFN-γ + IL-1β to model late insulitis in pancreatic β cells
Mireia Ramos-Rodríguez
Publication
Ramos-Rodríguez, M., Raurell-Vila, H., Colli, M.L. et al. The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes. Nat Genet. 51, 1588–1595 (2019) https://doi.org/10.1038/s41588-019-0524-6
Data availability
The different datasets that were used in the publication can be downloaded from GEO with the following accessions:
| GEO ID | Experiment | Link |
|---|---|---|
| GSE123404 | ATAC-seq | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123404 |
| GSE133135 | H3K27ac ChIP-seq | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133135 |
| GSE136865 | UMI-4C | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136865 |
| GSE137136 | RNA-seq | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137136 |
Data processing
ATAC-seq and H3K27ac CHIP-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/CYT/, in the source code repository for this website.