Raw RNA-seq count matrices from bovine oocytes matured under millifluidic and conventional in vitro conditions, and derived blastocysts

This dataset contains raw RNA sequencing read count matrices from two experiments investigating the effects of biomechanical stimulation during bovine in vitro oocyte maturation (IVM) on transcriptional profiles of matured oocytes and derived embryos.Oocyte data comprise raw counts from cumulus-oocyte complexes (COCs) matured under three culture conditions: (1) dynamic perfusion in a custom millifluidic device (OoTrap) at 20 µL h⁻¹, (2) static culture within the OoTrap device (no flow), and (3) conventional 2D culture in 4-well plates. Each condition includes five biological replicates, each consisting of 10 pooled MII oocytes. Libraries were prepared using the NEBNext Single Cell/Low Input cDNA Synthesis and Amplification Module and sequenced as 2x150 bp paired-end reads on an Illumina NovaSeq instrument.Blastocyst data comprise raw counts from individual expanded blastocysts (day 7) derived from oocytes matured under dynamic millifluidic or conventional 2D conditions. Four biological replicates per group were included. Libraries were prepared using the SMART-Seq HT Kit followed by Nextera XT library preparation and sequenced as 2x100 bp paired-end reads on an Illumina NovaSeq X Plus platform.All samples were derived from bovine (Bos taurus) ovaries obtained from a local abattoir. Raw counts were generated by mapping trimmed reads to the bovine reference genome (Ensembl) using STAR, with gene-level counts quantified via featureCounts. These matrices serve as the starting point for all differential expression and gene set enrichment analyses reported in the associated publication.