{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Rachel Scholey"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16575"],"description":["We aim to study the gene alteration in diabetic failing heart and decipher the molecular mechanisms underlying diabetes-associated heart failure. Diabetic patients are more vulnerable to cardiac dysfunction. The pathogenesis of diabetes-associated heart failure is multiple, including cardiac pathological remodeling, intracellular metabolic disorders, cardiac inflammation, etc. To determine which signaling pathways causes the myocardial alterations, we plan to identify the individual gene function during the pathogenesis using an unbiased large-scale screening. Firstly, gene expression should be assessed. RNA-seq is used to detect gene changes, afterwards, the potential candidates involved in the molecular basis induing diabetic heart failure will be validated by other assessment and function study will be performed to explore their role in the onset and progression of heart failure in diabetes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The hearts were collected and snap-frozen in liquid nitrogen at Baylor College of Medicine under proper licence and consent agreement; then imported under proper MTA and stored in -80 degree freezer with HTA licence before usage.","Library Construction - RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).","Sequencing - The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software.","Nucleic Acid Extraction - Total RNA from the heart tissue was extracted using TRIzol and treated with DNAse (ThermoFisher Scientific, AM1906) to eliminate genomic DNA contamination. The quality and integrity of total RNA samples were checked using a 2100 Bioanalyzer (Agilent Technologies)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Vicky Wei Liu","Rachel Scholey"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of heart tissue from patients with diabetes vs normal heart tissue","description":"We aim to study the gene alteration in diabetic failing heart and decipher the molecular mechanisms underlying diabetes-associated heart failure. Diabetic patients are more vulnerable to cardiac dysfunction. The pathogenesis of diabetes-associated heart failure is multiple, including cardiac pathological remodeling, intracellular metabolic disorders, cardiac inflammation, etc. To determine which signaling pathways causes the myocardial alterations, we plan to identify the individual gene function during the pathogenesis using an unbiased large-scale screening. Firstly, gene expression should be assessed. RNA-seq is used to detect gene changes, afterwards, the potential candidates involved in the molecular basis induing diabetic heart failure will be validated by other assessment and function study will be performed to explore their role in the onset and progression of heart failure in diabetes.","dates":{"release":"2026-02-20T00:00:00Z","modification":"2026-02-20T10:51:25.504Z","creation":"2026-01-26T12:08:16.692Z"},"accession":"E-MTAB-16575","cross_references":{"ENA":["ERP188136"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}