biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsShungo Kanetsukitranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16133Ulcerative colitis (UC) exhibits heterogeneous mucosal inflammation, and endocytoscopy allows real-time visualization of epithelial changes. This experiment investigated whether endocytoscopic inflammatory categories correspond to microRNA expression patterns. Colonic biopsy samples were collected from inflammatory and non-inflammatory sites in UC patients, along with non-IBD controls. Total RNA including small RNAs was extracted and hybridized to the Agilent Human miRNA Microarray (Design ID 021827). Normalized one-color intensity values were generated after background correction and quantile normalization. The study aimed to define mucosal microRNA signatures associated with UC inflammatory status.biostudies-arrayexpressSample Collection - Colonic mucosal biopsy samples were obtained endoscopically from patients with ulcerative colitis (UC) and from non-IBD controls during routine colonoscopy. For UC patients, biopsies were collected from both inflammatory (IA) and non-inflammatory (NIA) sites as assessed endoscopically. Control samples were collected from normal-appearing mucosa. Biopsy specimens were immediately placed in RNAlater and stored at −80°C until RNA extraction.Labeling - Labeling of small RNAs was performed using the Agilent miRNA Complete Labeling and Hyb Kit. Total RNA was dephosphorylated, denatured, and labeled with Cy3-pCp using T4 RNA ligase following the manufacturer’s protocol. The labeled RNA was purified prior to hybridization.Hybridization - Labeled miRNA samples were hybridized onto the Agilent Human miRNA Microarray Release 16.0 (Design ID 021827) using the Agilent SureHyb system. Hybridization was carried out at 55°C for 20 hours according to the Agilent miRNA microarray hybridization protocol. After hybridization, slides were washed using the Agilent miRNA Wash Buffer system.Scaning - Microarrays were scanned using the Agilent DNA Microarray Scanner (model G2565CA) at 5 µm resolution. Fluorescence signal intensities were extracted using Agilent Feature Extraction Software (version 10.7.3.1) with default miRNA extraction settings.Nucleic Acid Extraction - Total RNA, including small RNAs, was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Tissue samples were homogenized, and RNA was purified using silica-membrane columns. RNA concentration and purity were determined by UV absorption (NanoDrop), and RNA integrity was assessed using the Agilent 2100 Bioanalyzer.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsShungo KanetsukiData Transformation - Raw signal intensities were background-corrected and normalized using the quantile normalization algorithm within Agilent GeneSpring GX software. Probes not detected above background were marked as “NA”. Normalized one-color signal intensities were used for downstream statistical analysis and for submission to ArrayExpress as processed data.falseEndocytoscopic Classification is Associated with a MicroRNA-Based Inflammatory Signature in Ulcerative ColitisUlcerative colitis (UC) exhibits heterogeneous mucosal inflammation, and endocytoscopy allows real-time visualization of epithelial changes. This experiment investigated whether endocytoscopic inflammatory categories correspond to microRNA expression patterns. Colonic biopsy samples were collected from inflammatory and non-inflammatory sites in UC patients, along with non-IBD controls. Total RNA including small RNAs was extracted and hybridized to the Agilent Human miRNA Microarray (Design ID 021827). Normalized one-color intensity values were generated after background correction and quantile normalization. The study aimed to define mucosal microRNA signatures associated with UC inflammatory status.2026-01-31T00:00:00Z2026-05-27T15:52:25.003Z2025-11-14T14:01:36.524ZE-MTAB-16133EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815