biostudies-arrayexpressJacopo SabbatinelliHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16866Systemic sclerosis (SSc) is a complex autoimmune disease characterized by microvascular dysfunction, immune dysregulation, and progressive fibrosis, and can be classified into limited cutaneous (lcSSc) and diffuse cutaneous (dcSSc) forms. Primary Raynaud’s phenomenon (RP) is a functional vascular disorder that may precede or occur independently of connective tissue diseases. Circulating microRNAs (miRNAs) have emerged as regulators of vascular and immune processes and can be detected in serum. In this study, serum miRNA profiles were assessed in patients with SSc, including lcSSc and dcSSc subtypes, RP, and healthy controls. Small RNA sequencing was performed in a discovery cohort to characterize circulating miRNA expression across the study groups. Libraries were prepared from serum-derived RNA and sequenced on an Illumina platform. Raw sequencing data were processed using a standardized pipeline for miRNA quantification, and normalized counts were generated for downstream analyses. This dataset provides a resource for the exploration of circulating miRNA profiles in SSc subtypes and RP.biostudies-arrayexpressLibrary Construction - Small RNA sequencing libraries were prepared from 5 μl of plasma RNA using the QIAseq miRNA Library Kit (catalog no. 331505, Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The quality and concentration of libraries were determined using the High Sensitivity DNA ScreenTape Analysis on the TapeStation 4150 system (Agilent Technologies, Santa Clara, CA, USA).Sample Collection - Peripheral blood samples were collected in clot activator gel tubes (BD, United Kingdom), allowed to clot at room temperature, and then centrifuged to obtain serum, which was aliquoted and stored at −80 °C until analysis.Nucleic Acid Extraction - After two subsequent spins, total RNA, including small (< 200 nucleotides) RNAs, was extracted from serum using Norgen’s total RNA Purification Kit (cat. no. 37500, Norgen Biotek Corporation, Canada) according to the manufacturer’s protocol. Purified RNA was stored at −80°C until analysis.Sequencing - Libraries were diluted to 1.5 pM and sequenced using the NextSeq 500/550 High Output Kit v2.5 75-cycle flow cell (Illumina, San Diego, CA, USA) on the NextSeq 500 platform (Illumina).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Sequencing raw data (FASTQ) were analyzed using the QIAseq miRNA Primary Quantification pipeline via the GeneGlobe Data Analysis Center.UnknownTranscriptomicsNextSeq 550RNA-seq of non coding RNAHomo sapiensTatiana SpadoniSilvia Svegliati BaroniJacopo SabbatinelliGianluca MoroncinifalseSmall RNA-seq analysis of serum miRNAs from patients with systemic sclerosis, Raynaud’s phenomenon, and healthy controlsSystemic sclerosis (SSc) is a complex autoimmune disease characterized by microvascular dysfunction, immune dysregulation, and progressive fibrosis, and can be classified into limited cutaneous (lcSSc) and diffuse cutaneous (dcSSc) forms. Primary Raynaud’s phenomenon (RP) is a functional vascular disorder that may precede or occur independently of connective tissue diseases. Circulating microRNAs (miRNAs) have emerged as regulators of vascular and immune processes and can be detected in serum. In this study, serum miRNA profiles were assessed in patients with SSc, including lcSSc and dcSSc subtypes, RP, and healthy controls. Small RNA sequencing was performed in a discovery cohort to characterize circulating miRNA expression across the study groups. Libraries were prepared from serum-derived RNA and sequenced on an Illumina platform. Raw sequencing data were processed using a standardized pipeline for miRNA quantification, and normalized counts were generated for downstream analyses. This dataset provides a resource for the exploration of circulating miRNA profiles in SSc subtypes and RP.2026-04-01T00:00:00Z2026-04-07T12:00:34.04Z2026-04-07T12:00:02.654ZE-MTAB-16866ERP191817EFO_0003737EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0004184