Integrated miRNA expression dataset in ruminant hosts naturally infected with cystic echinococcosis

Cystic echinococcosis is a zoonotic infection caused by the larval stage of Echinococcus granulosus sensu lato and remains endemic in several livestock-producing regions. This article describes a dataset of microRNA (miRNA) profiles obtained using Echinococcus cyst material collected from naturally infected sheep, cattle, and water buffalo in southern Italy, providing a valuable resource for the characterization and comparative analysis of miRNA profiles across different ruminant host species. The dataset includes 38 samples obtained from different cyst matrices, including 10 protoscoleces (PSCs), 11 fertile and 17 sterile germinal membranes. Total RNA was extracted and processed using high-throughput sequencing technology. Raw sequence data, quality-filtered reads, and annotated miRNA entries are provided. A total of 168 mature molecules were identified using standardized bioinformatics workflows, including quality control, adapter removal, sequence alignment, annotation against reference databases, normalization procedures, and differential expression analysis. Raw fastq files are publicly available in the Sequence Read Archive under accession SUB16008388. Supplementary Tables provide raw and normalized counts for each sample, together with information on host species, cyst localization, biological matrix, fertility status, and sample quality parameters. Sequencing metrics include raw reads, retained reads following processing and adapter trimming, percentage of reads retained, and the number of mature miRNAs detected. Differential expression results are also provided for fertile vs sterile membranes, PSCs vs fertile membranes and PSCs vs sterile membranes. Overall, this dataset provides a comprehensive small RNA-Seq resource supporting studies of parasite developmental biology, host-associated variation, molecular marker discovery, comparative omics analyses, and the development of bioinformatics workflows.