{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Timothy Pullen"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-12382"],"description":["Type 1 diabetes (T1D) is characterised by destruction of pancreatic beta cells by islet-infiltrating cytotoxic lymphocytes, and elevated intra-islet secretion of pro-inflammatory cytokines. We hypothesise that abnormal elevation of islet NAD, via activation of NAMPT, plays a key role in driving islet autoimmune processes in T1D. In vitro, the NAMPT inhibitor FK866 protected mouse and human islets against cytokine-mediated beta cell dysfunction and death. We used RNA-Seq to dissect the transcriptional response of mouse islets subjected in vitro to cytokines in the presence and absence of FK866."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Isolated islets were maintained in supplemented RPMI at 37 °C and 5% CO2 in a humidified atmosphere for up to 24 hours prior to experimental treatment.","Sequencing - Libraries were pooled at equal molar ratio and sequenced using an Illumina NovaSeq 6000 at 150bp paired end with an approximated depth of 25 million reads per sample.","Library Construction - 100ng total RNA from each sample was used as input to generate library for RNAseq. RNAseq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs, Hertfordshire, UK. Cat.no: E7760) following manufacturer’s recommendations.","Sample Treatment - Isolated mouse islets were subjected for 24 h to (A) no treatment, (B) a cytokine cocktail (IL-1β, TNFα and IFNγ; 1 ng/ml) or (C) FK866 (10 nM) and cytokine cocktail.","Sample Collection - Mouse islets were isolated between 10:00 and 11:00 hours. Pancreata were inflated with 1mg/mL collagenase solution (Sigma-Aldrich, Poole, U.K.) followed by density gradient separation (Histopaque-1077; Sigma-Aldrich).","Nucleic Acid Extraction - Total RNA was extracted from ∼150 islets per mouse, according to the manufacturer's instructions (RNeasy Mini Kit, Qiagen, UK)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Timothy Pullen","Paul Caton","Daniel Egbase"],"additional_accession":[]},"is_claimable":false,"name":"RNA-Seq of mouse pancreatic islets treated with cytokines and NAMPT inhibitor (FK866)","description":"Type 1 diabetes (T1D) is characterised by destruction of pancreatic beta cells by islet-infiltrating cytotoxic lymphocytes, and elevated intra-islet secretion of pro-inflammatory cytokines. We hypothesise that abnormal elevation of islet NAD, via activation of NAMPT, plays a key role in driving islet autoimmune processes in T1D. In vitro, the NAMPT inhibitor FK866 protected mouse and human islets against cytokine-mediated beta cell dysfunction and death. We used RNA-Seq to dissect the transcriptional response of mouse islets subjected in vitro to cytokines in the presence and absence of FK866.","dates":{"release":"2025-11-22T00:00:00Z","modification":"2025-11-22T02:02:33.369Z","creation":"2022-11-22T17:29:06.091Z"},"accession":"E-MTAB-12382","cross_references":{"ENA":["ERP142749"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003738","EFO_0004184","EFO_0003969"]}}