Multi-omics data compendium: Data package 11 (Pck011)

Sarkar, Soumyadeep; Flores, Javier E; Nune, Navaj; Ramos-Rodriguez, Mireia; Kulkarni, Abhishek; Ives, Ashley N; Hammoud, Batoul; Wu, Wenting; Yi, Xiaoyan; Roca-Rivada, Arturo; Maestas, Marlie M; Gluth, Austin; Elliott, Emily C; You, Youngki; Krishnan, Preethi; Syed, Farooq; Kim, Young-Mo; Kyle, Jennifer E; Kono, Tatsuyoshi; Fulcher, James M; Sims, Emily K; Tersey, Sarah A; Sussel, Lori; Webb-Robertson, Bobbie-Jo M; Qian, Weijun; Zhang, Tong; Metz, Thomas O; Millman, Jeffrey R; Evans-Molina, Carmella; Pasquali, Lorenzo; Mirmira, Raghavendra G; Eizirik, Decio L; Nakayasu, Ernesto S

doi:10.25584/3012057

Title: Multi-omics data compendium: Data package 11 (Pck011)

Dataset
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Abstract

In type 1 diabetes (T1D), autoimmune response and inflammation cause the death of pancreatic ß cells, leading to the body’s inability to produce insulin and maintain glucose homeostasis. This process is at least in part mediated by pro-inflammatory cytokines, such as interferon (IFN)a, IFN?, interleukin (IL)-1ß, and tumor necrosis factor (TNF)a, which induce ß-cell dysfunction and apoptosis. A deep understanding of the ß-cell signaling and regulatory networks induced by these cytokines could lead to the identification of therapeutic targets to prevent T1D development. To study cytokine-mediated islets/ß-cell signaling and regulatory networks, a variety of omics experiments have been conducted, including transcriptomics, epigenomics (DNA methylation, UMI-4C, ATAC-seq & ChIP-seq), proteomics (bottom-up, top-down, post-translational modification analysis), lipidomics, and metabolomics. The combination of these datasets can be instrumental in identifying signaling components and regulatory factors involved in ß-cell stress/death. Here, we aggregated these multiple omics datasets into a centralized location, providing a quality-controlled and statistically rigorous resource for investigators seeking to holistically study ß-cell regulation by pro-inflammatory cytokines.

Authors:

Sarkar, Soumyadeep; Flores, Javier E; Nune, Navaj; Ramos-Rodriguez, Mireia; Kulkarni, Abhishek; Ives, Ashley N; Hammoud, Batoul; Wu, Wenting; Yi, Xiaoyan; Roca-Rivada, Arturo; Maestas, Marlie M; Gluth, Austin; Elliott, Emily C; You, Youngki; Krishnan, Preethi; Syed, Farooq;

; Kyle, Jennifer E; Kono, Tatsuyoshi; Fulcher, James M more »

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
University Pompeu Fabra
University of Chicago
Indiana University School of Medicine
ULB
Université Libre de Bruxelles
Washington University School of Medicine
Washington State University Tri-Cities
University of Colorado

Publication Date:: Sun Dec 28 19:00:00 EST 2025

DOE Contract Number:: AC05-76RL01830

Research Org.:: PNNL (PNNL2)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 3012057

DOI:: https://doi.org/10.25584/3012057

Citation Formats


                    Sarkar, Soumyadeep, Flores, Javier E, Nune, Navaj, Ramos-Rodriguez, Mireia, Kulkarni, Abhishek, Ives, Ashley N, Hammoud, Batoul, Wu, Wenting, Yi, Xiaoyan, Roca-Rivada, Arturo, Maestas, Marlie M, Gluth, Austin, Elliott, Emily C, You, Youngki, Krishnan, Preethi, Syed, Farooq, Kim, Young-Mo, Kyle, Jennifer E, Kono, Tatsuyoshi, Fulcher, James M, Sims, Emily K, Tersey, Sarah A, Sussel, Lori, Webb-Robertson, Bobbie-Jo M, Qian, Weijun, Zhang, Tong, Metz, Thomas O, Millman, Jeffrey R, Evans-Molina, Carmella, Pasquali, Lorenzo, Mirmira, Raghavendra G, Eizirik, Decio L, and Nakayasu, Ernesto S. Multi-omics data compendium: Data package 11 (Pck011).  United States: N. p., 2025. 
        Web.  doi:10.25584/3012057.

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                    Sarkar, Soumyadeep, Flores, Javier E, Nune, Navaj, Ramos-Rodriguez, Mireia, Kulkarni, Abhishek, Ives, Ashley N, Hammoud, Batoul, Wu, Wenting, Yi, Xiaoyan, Roca-Rivada, Arturo, Maestas, Marlie M, Gluth, Austin, Elliott, Emily C, You, Youngki, Krishnan, Preethi, Syed, Farooq, Kim, Young-Mo, Kyle, Jennifer E, Kono, Tatsuyoshi, Fulcher, James M, Sims, Emily K, Tersey, Sarah A, Sussel, Lori, Webb-Robertson, Bobbie-Jo M, Qian, Weijun, Zhang, Tong, Metz, Thomas O, Millman, Jeffrey R, Evans-Molina, Carmella, Pasquali, Lorenzo, Mirmira, Raghavendra G, Eizirik, Decio L, & Nakayasu, Ernesto S. Multi-omics data compendium: Data package 11 (Pck011).  United States.  doi:https://doi.org/10.25584/3012057

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                    Sarkar, Soumyadeep, Flores, Javier E, Nune, Navaj, Ramos-Rodriguez, Mireia, Kulkarni, Abhishek, Ives, Ashley N, Hammoud, Batoul, Wu, Wenting, Yi, Xiaoyan, Roca-Rivada, Arturo, Maestas, Marlie M, Gluth, Austin, Elliott, Emily C, You, Youngki, Krishnan, Preethi, Syed, Farooq, Kim, Young-Mo, Kyle, Jennifer E, Kono, Tatsuyoshi, Fulcher, James M, Sims, Emily K, Tersey, Sarah A, Sussel, Lori, Webb-Robertson, Bobbie-Jo M, Qian, Weijun, Zhang, Tong, Metz, Thomas O, Millman, Jeffrey R, Evans-Molina, Carmella, Pasquali, Lorenzo, Mirmira, Raghavendra G, Eizirik, Decio L, and Nakayasu, Ernesto S. 2025.  
"Multi-omics data compendium: Data package 11 (Pck011)".  United States.  doi:https://doi.org/10.25584/3012057.  https://www.osti.gov/servlets/purl/3012057. Pub date:Sun Dec 28 19:00:00 EST 2025

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@article{osti_3012057,

  title        = {Multi-omics data compendium: Data package 11 (Pck011)},

  author       = {Sarkar, Soumyadeep and Flores, Javier E and Nune, Navaj and Ramos-Rodriguez, Mireia and Kulkarni, Abhishek and Ives, Ashley N and Hammoud, Batoul and Wu, Wenting and Yi, Xiaoyan and Roca-Rivada, Arturo and Maestas, Marlie M and Gluth, Austin and Elliott, Emily C and You, Youngki and Krishnan, Preethi and Syed, Farooq and Kim, Young-Mo and Kyle, Jennifer E and Kono, Tatsuyoshi and Fulcher, James M and Sims, Emily K and Tersey, Sarah A and Sussel, Lori and Webb-Robertson, Bobbie-Jo M and Qian, Weijun and Zhang, Tong and Metz, Thomas O and Millman, Jeffrey R and Evans-Molina, Carmella and Pasquali, Lorenzo and Mirmira, Raghavendra G and Eizirik, Decio L and Nakayasu, Ernesto S},

  abstractNote = {In type 1 diabetes (T1D), autoimmune response and inflammation cause the death of pancreatic ß cells, leading to the body’s inability to produce insulin and maintain glucose homeostasis. This process is at least in part mediated by pro-inflammatory cytokines, such as interferon (IFN)a, IFN?, interleukin (IL)-1ß, and tumor necrosis factor (TNF)a, which induce ß-cell dysfunction and apoptosis. A deep understanding of the ß-cell signaling and regulatory networks induced by these cytokines could lead to the identification of therapeutic targets to prevent T1D development. To study cytokine-mediated islets/ß-cell signaling and regulatory networks, a variety of omics experiments have been conducted, including transcriptomics, epigenomics (DNA methylation, UMI-4C, ATAC-seq & ChIP-seq), proteomics (bottom-up, top-down, post-translational modification analysis), lipidomics, and metabolomics. The combination of these datasets can be instrumental in identifying signaling components and regulatory factors involved in ß-cell stress/death. Here, we aggregated these multiple omics datasets into a centralized location, providing a quality-controlled and statistically rigorous resource for investigators seeking to holistically study ß-cell regulation by pro-inflammatory cytokines.},

  doi          = {10.25584/3012057},

  journal      = {},

  number       = ,

  volume       = ,

  place        = {United States},

  year         = {Sun Dec 28 19:00:00 EST 2025},

  month        = {Sun Dec 28 19:00:00 EST 2025}

}

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DOI: https://doi.org/10.25584/3012057

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