{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Christopher Smith"],"organism":["Mus musculus"],"software":["cutadapt (v3.4), STAR (v2.7.3a)","featureCounts (v2.0.3)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16104"],"description":["Patients with type 2 diabetes often experience many years of reduced β-cell function and impaired glucose tolerance preceding diabetes diagnosis. It is postulated that β-cell function may be compromised by relatively small changes in glycaemia, initiating a gradual decline that underlies diabetes progression. It has been widely reported that chronic hyperglycaemia/diabetes alters the expression of multiple genes involved in glucose metabolism in both rodent and human islets. We therefore investigated the extent to which impaired glucose tolerance (IGT) and chronic mild and severe hyperglycaemia (HG) impact gene expression in mouse β-cells. Gene expression was measured in primary islets isolated from control, IGT, mild HG and severe HG mice by bulk RNAseq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Mice were killed by cervical dislocation, pancreata were inflated with collagenase solution at 1 mg/ml, resected and placed in a water bath at 37°C for 10 min. After washing, islets were purified on a Histopaque-1119 / Histopaque-1083 gradient. Islets were cultured overnight at 37oC and 5% CO2 for respirometry, insulin secretion and enzyme studies, but were lysed ~3-4 hours after isolation for RNAseq analysis.","Nucleic Acid Extraction - Total RNA was isolated from islets using the ReliaPrep™ RNA Cell Miniprep System (Promega), according to the manufacturer’s instructions. RNA quality was validated using an Agilent Bioanalyzer 2100. All samples had RIN values between 7.4 to 10.","Library Construction - 500 ng of total RNA was used for library construction using Illumina’s TruSeq Stranded mRNA prep kit following the manufacturer’s instructions. Indexed libraries were purified and validated using an Agilent Bioanalyzer 2100. Sequencing libraries were pooled at equal molar concentration.","Sequencing - Paired-end sequencing was performed on an Illumina NovaSeq 6000 instrument."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Quality and adaptor trimming of sequenced transcripts was performed using cutadapt (v3.4). STAR (v2.7.3a) was used to align transcripts to the mouse genome (GRCm38).","Data Transformation - Raw counts were generated using featureCounts (v2.0.3)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Frances Ashcroft","Fiona Gribble","Elizabeth Haythorne","Christopher Smith"],"additional_accession":[]},"is_claimable":false,"name":"Bulk transcriptomic analysis of primary beta cells from control, IGT, mild, and severely diabetic mice.","description":"Patients with type 2 diabetes often experience many years of reduced β-cell function and impaired glucose tolerance preceding diabetes diagnosis. It is postulated that β-cell function may be compromised by relatively small changes in glycaemia, initiating a gradual decline that underlies diabetes progression. It has been widely reported that chronic hyperglycaemia/diabetes alters the expression of multiple genes involved in glucose metabolism in both rodent and human islets. We therefore investigated the extent to which impaired glucose tolerance (IGT) and chronic mild and severe hyperglycaemia (HG) impact gene expression in mouse β-cells. Gene expression was measured in primary islets isolated from control, IGT, mild HG and severe HG mice by bulk RNAseq.","dates":{"release":"2025-12-31T00:00:00Z","modification":"2026-05-27T17:36:19.518Z","creation":"2025-11-12T08:02:44.11Z"},"accession":"E-MTAB-16104","cross_references":{"ENA":["ERP184248"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}