MassIVE MSV000093466

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Protection of beta cells against pro-inflammatory cytokine stress by GDF15-ERBB2 signaling

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Description

TMT-labeled proteomic data from human islets treated with or without GDF15 for 24 h followed by cytokine (IL1beta & IFNgamma) treatment for 24 h. There are 4 biological replicates. Islets were collected and dissolved in 50 mM NH4HCO3 containing 8 M urea, digested with trypsin and labeled with a 16-plex TMT kit. Peptides were multiplexed, fractionated by high pH reverse phase chromatography, and analyzed by LC-MS/MS on an Acquity M-Class Nano UHPLC system connected to a Q-Exactive mass spectrometer. LC-MS/MS data were processed with MaxQuant, by searching against a human SwissProt database (2017-04-12 with 20,198 proteins). The default settings for precursor and fragment mass tolerance were used. Peptide searching was performed with specific trypsin digestion with a maximum of two missed cleavage sites. Carbamidomethylation of cysteine was set as a fixed modification; acetylation of protein N-terminus and oxidation of methionine residues were set as variable modifications. The false discovery rate (FDR) was set to 1% at the protein and peptide levels. The dataset was log2 transformed, and sample level quality control was performed to ensure that all of the samples had data of high enough quality for analyses. With no sample-level issues identified, the data was normalized to total abundance. Statistical analyses utilized a standard Analysis of Variance (ANOVA) model. [doi:10.25345/C58912225] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: GDF15 ; ERBB2 ; HER2

Contact

Principal Investigators:
(in alphabetical order) 		Ernesto S. Nakayasu, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt

Publications

Soumyadeep Sarkar, Farooq Syed, Bobbie-Jo Webb-Robertson, John T. Melchior, Garrick Chang, Marina Gritsenko, Yi-Ting Wang, Chia-Feng Tsai, Jing Liu, Xiaoyan Yi, Yi Cui, Decio L. Eizirik, Thomas O. Metz, Marian Rewers, Carmella Evans-Molina, Raghavendra G. Mirmira, Ernesto S. Nakayasu.
Protection of ? cells against pro-inflammatory cytokine stress by the GDF15-ERBB2 signaling.
doi: 10.1101/2023.11.27.23298904v1.

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