Dataset - Proteomics, Transcriptomics, Metabolomics, Lipidomics, ChIP-seq Multi-omics data compendium: Data package 2 (Pck002)

This data package consists of data from parallel experiments compared to Pck001 but performed with EndoC-βH1 cells instead of human islets. Cells were treated with IFNγ + IL-1β for 48 h and submitted to RNA-seq (n=5), ATAC-seq (n=5), DNA methylation (n=5), and H3K27Ac ChIP-seq (n=4). In addition, proteomics, lipidomics, and metabolomics were performed in a batch of cells (n=3) (Table 1).

Data contributors:

Mireia Ramos-Rodríguez & Lorenzo Pasquali: Endocrine Regulatory Genomics, Department of Experimental & Health Sciences, University Pompeu Fabra, Barcelona, 08003, Spain.

Ernesto S. Nakayasu, Jennifer Kyle, Young-Mo Kim, Soumyadeep Sarkar & Thomas O. Metz: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.

Farooq Syed: Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA & Department of Diabetes Immunology, Beckman Research Institute, City of Hope, Duarte, CA, USA.

Rahavendra Mirmira: Kovler Diabetes Center and Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.

Data repositories:

RNA-seq: GSE137136

ATAC-seq: GSE123404

Proteomics: PXD011902

Lipidomics: MSV000086174

Metabolomics: https://osf.io/nskdc

DNA methylation: https://doi.org/10.5281/zenodo.17530197

H3K27ac ChIP-seq: GSE133135

Publications: PMID 31676868 & PMID 38383396