{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jean-Philippe Cartailler"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14642"],"description":["Sustained stimulation and elevations in intracellular Ca2+ concentrations due to metabolic stress in pre-diabetic states triggers gene expression changes contributing to the loss of pancreatic β-cell function. To establish a temporal relationship between β-cell stimulation and perturbations in  Ca2+-dependent transcription, islet  Ca2+ dynamics and gene expression was analysed in cultured mouse islets that were stimulated by membrane depolarization with tolbutamide, a sulfonylurea that blocks the ATP-dependent potassium (KATP) channel. By varying the timing and nature of the experimental stimulory conditions, we defined temporal transcriptional dynamics of islets in responce to stimulation,  identified immediate early response genes and transcriptional regulators that drive these transcriptional changes and defined a set of physiologically relevant  Ca2+-regulated genes with sustained changes 24 hours post-stimulation.  Ca2+-dependent changes resulting from chronic stimulation include an increase in β-cell stress response and dedifferentiation genes, and a decrease in critical β-cell identity genes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted from isolated mouse pancreatic islets using Maxwell simplyRNA kits (Promega).","Sequencing - Libraries were subjected to 150 bp paired-end sequencing using Illumina NovaSeq6000 system at Novogene.","Library Construction - cDNA libraries were constructed using low input Illumina library prep workflow at Novogene.","Sample Collection - Male mice were used for islet isolations at 8-9 weeks of age. Mouse islets were isolated following an injection of 0.6 mg/mL Collagenase P (Roche) into the pancreatic bile duct. Partially dissociated tissue was fractionated using a Histopaque-1077 (Sigma) gradient followed by hand-picking of islets. Islets were incubated in vitro following the treatment protocol and then used for RNA isolations.","Sample Treatment - C57BL/6J mice fed regular chow (4.5% fat content, PicoLab, 5L0D) were used for all experiments. Ascl1β knockout (KO) mice were obtained by interbreeding animals with the Ascl1tm2Fgu, Ins1tm1.1(cre)Thor and Gt(ROSA)26Sortm9(CAG-tdTomato)Hze alleles. Mouse islets were isolated at 8-9 weeks of age. Isolated islets were cultured overnight (16 hours) in islet culture media consisting of low (1 mg/L) glucose DMEM (Thermo, 11966-025) supplemented with 10% FBS (Atlanta Biologicals), 4.6 mM HEPES, 1% penicillin/streptomycin (Thermo), 1% non-essential amino acids (Sigma) in 24-well plates at 37°C with 5% CO2 infusion and 95% humidity. For time series experiments, wild type islets were treated with culture media containing 100 μM tolbutamide (Sigma, T0891) for 0 hours (control), 0.5 hours, 2 hours, 6 hours, and 24 hours and then collected for RNA isolations.   For combinatorial treatment experiments, islets were treated for 24 hours as following: 1) with 100 μM tolbutamide (Sigma, T0891); 2) with combination of 100 μM tolbutamide and 50 μM verapamil (Sigma, V4629); 3) with combination of 100 μM tolbutamide (Sigma, T0891) and 1 μM CREB-inhibitor 666-15 (MedChemExpress, HY-101120); with high glucose (20 mM),  Control samples were treated only with the DMSO vehicle (0.1%). Islets from Ascl1βKO mice were treated for 24 hours with tolbutamide."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The Spliced Transcripts Alignment to a Reference (STAR v2.6.0c) application (Dobin, Davis et al. 2013) was used to perform sequence alignments to the mm10 (GRCm38) mouse genome reference and GENCODE comprehensive gene annotations (Release M17). STAR’s two-pass mapping approach was used to increase the detection of reads mapping to novel junctions identified during the first mapping pass.","Data Transformation - DESeq2 was employed, which uses raw counts and models the normalization inside the Generalized Linear Model (GLM)"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["<h4>Article highlights</h4>This study was undertaken to establish a temporal link between an increase in intracellular Ca2+ concentration and the loss of pancreatic β-cell identity. We profiled the alterations in Ca2+ dynamics and gene transcription that occur in freshly isolated islets following membrane depolarization. We show that initially adaptive Ca2+-dependent transcription changes, mediated largely by CREB and CREB-dependent transcription factors, rapidly become maladaptive, causing the loss of β-cell identity and function. We also show that many effector genes linked to nearby human type 2 diabetes susceptibility loci are regulated by Ca2+-dependent mechanisms."],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["Dynamic Ca2+-Dependent Transcription Links Metabolic Stress to Impaired β-Cell Identity."],"pubmed_authors":["Anna Osipovich","Osipovich AB, Dickerson MT, Cartailler JP, Shrestha S, Wright NM, Jacobson DA, Magnuson MA.","Jean-Philippe Cartailler","Mark Magnuson","Shristi Shrestha"],"additional_accession":[]},"is_claimable":false,"name":"Dynamic Ca2+-dependent transcription links metabolic stress to impaired β-cell identity","description":"Sustained stimulation and elevations in intracellular Ca2+ concentrations due to metabolic stress in pre-diabetic states triggers gene expression changes contributing to the loss of pancreatic β-cell function. To establish a temporal relationship between β-cell stimulation and perturbations in  Ca2+-dependent transcription, islet  Ca2+ dynamics and gene expression was analysed in cultured mouse islets that were stimulated by membrane depolarization with tolbutamide, a sulfonylurea that blocks the ATP-dependent potassium (KATP) channel. By varying the timing and nature of the experimental stimulory conditions, we defined temporal transcriptional dynamics of islets in responce to stimulation,  identified immediate early response genes and transcriptional regulators that drive these transcriptional changes and defined a set of physiologically relevant  Ca2+-regulated genes with sustained changes 24 hours post-stimulation.  Ca2+-dependent changes resulting from chronic stimulation include an increase in β-cell stress response and dedifferentiation genes, and a decrease in critical β-cell identity genes.","dates":{"release":"2025-05-22T00:00:00Z","modification":"2025-06-23T12:01:13.626Z","creation":"2024-11-29T17:56:12.616Z"},"accession":"E-MTAB-14642","cross_references":{"pubmed":["40526459"],"ENA":["ERP166672"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"],"doi":["10.2337/db24-1141"]}}