biostudies-arrayexpressAdelina Lopez Lopez JaraSus scrofahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16983The objective of this study was to evaluate the effects of eCG administered alone or in combination with buserelin (BU) on ovulatory response, embryo production efficiency, developmental synchrony, and blastocyst transcriptomic profiles in weaned donor sows. The experiment comprised six trials, each conducted over a 1-week period with 8-14 sows. A total of 76 sows selected at weaning were randomly assigned to three experimental group: eCG group (n = 27); eCG + BU group (n = 29); and control group (n = 20). Sows in the eCG group received 1000 IU of equine chorionic gonadotropin (eCG, Folligon®, Intervet International B.V., Boxmeer, The Netherlands) 24 hours post-weaning to induce superovulation. Sows in the eCG + BU group received the same eCG treatment, followed by 10 µg of BU (2.5 mL Receptal®, Merck Sharp & Dohme Animal Health, S.L., Salamanca, Spain) at the onset of estrus. Control sows received no hormonal estimulation and were monitored for spontaneous estrus post-weaning. In vivo-developed embryos were surgically recovered on Day 6 after estrus. Four independent pools of 5 viable blastocysts per group (total n=20 blastocysts per group) were prepared for transcriptome analysis. Embryos were placed in sterile microcentrifuge tubes with 5 µL of PBS, immediately immersed in LN2 and stored at -80 °C until RNA extraction and subsequent RNA-seq analysis. After analysis, data were processed and normalized, and differentially expressed genes (DEGs) were identified for each hormonal treatment compared with the control. DEG lists were compared to identify treatment-specific gene expression changes. Pathway enrichment analysis was performed for each DEG list.biostudies-arrayexpressLibrary Construction - Strand-specific RNA-seq libraries were prepared using Total RNA Prep Ligation with Ribo Zero Plus kit (Illumina; Cat. No. 20040525). Library preparation included depletion of ribosomal RNA, fragmentation of the remaining RNA, and synthesis of double-stranded cDNA. Libraries were completed through end repair, adapter ligation, PCR enrichment, and a cleanup step to eliminate small fragments and adapter dimers. Library size distribution was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).Sample Treatment - Treatment protocol eCG+BU Multiparous sows (LandracexLarge-White) of parity 4 to 6 were used as embryo donors. Animals were housed in individual crates within a mechanically ventilated building and received a standard commercial diet twice daily with free access to water. In this protocol sows received 1000 IU of equine chorionic gonadotropin (eCG, Folligon®, Intervet International B.V., Boxmeer, The Netherlands) 24 hours post-weaning, followed by 10 µg of BU (2.5 mL Receptal®, Merck Sharp & Dohme Animal Health, S.L., Salamanca, Spain) at the onset of estrus.Sample Treatment - Control treatment Multiparous sows (LandracexLarge-White) of parity 4 to 6 were used as embryo donors. Animals were housed in individual crates within a mechanically ventilated building and received a standard commercial diet twice daily with free access to water. In this case, control sows received no hormonal stimulation and were monitored for spontaneous estrus post-weaningNucleic Acid Extraction - Nucleic acid extraction protocol: Extraction of RNA from blastocyst samples was carried out by using a miRNeasy Micro Kit (Qiagen Ibérica, Madrid, Spain) according to the manufacturer´s instructions. RNA concentration and purity were measured on a NanoDrop 2000 (Thermo Fisher Scientific, Madrid, Spain). RNA integrity was then examined with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Only high-quality preparations (RIN > 8) were taken forward for library construction.Sample Collection - Embryos were recovered via midline laparotomy on Day 6 of the estrous cycle (D0=onset of estrus). Sows were sedated with azaperone (2 mg/kg body weight, intramuscular) and then give sodium thiopental (7 mg/kg body weight, intravenous) to induce general anesthesia and maintained with isoflurane (3.5-5%). The ovaries and uterine horns were exposed through a mid-ventral incision and the number of corpora lutea was immediately counted to assess the response to hormonal stimulation, and ovulatory response was quantified. Embryo collection was carried out by flushing the proximal 50 cm of each uterine horn with 30 mL of recovery medium (mTL-HEPES-PVA). After collection, the embryos were evaluated for morphological quality and stage of development, and only embryos at the blastocyst stage with appropriate morphology were selected for the experiment.Sequencing - Libraries were sequenced on a NextSeq 500 (Illumina) using a High Output v2.5 kit (150 cycles), producing paired-end reads of 75 bp from each end (2 × 75 bp). Sequencing files were analysed in Partek Flow (Illumina). Reads were trimmed to remove adapter contamination and low-quality sequence, and post-trimming QC was used to confirm read quality and composition. Alignment was performed against the Sus scrofa genome assembly Sscrofa11.1 using STAR (Dobin et al., 2013), with the default RNA seq settings in Partek Flow. Gene counts were summarized at the gene level using the reference annotation model. Differential expression was tested with DESeq2 after median-of-ratios normalization. Differential expression was considered significant at a Benjamini–Hochberg adjusted false discovery rate (FDR) < 0.05 combined with an absolute fold change ≥ 1.5. Functional over-representation of GO terms and KEGG pathways among significant genes was assessed in Partek Flow with a hypergeometric test. Protein–protein interaction (PPI) networks were generated using the STRING database to explore functional associations among the identified DEGs.Sample Treatment - Treatment protocol eCG Multiparous sows (LandracexLarge-White) of parity 4 to 6 were used as embryo donors. Animals were housed in individual crates within a mechanically ventilated building and received a standard commercial diet twice daily with free access to water. In this protocol sows received 1000 IU of equine chorionic gonadotropin (eCG, Folligon®, Intervet International B.V., Boxmeer, The Netherlands) 24 hours post-weaning.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Load raw FASTQ files from Sus scrofa embryos into Partek Flow and perform quality control. Align reads to the Sus scrofa reference genome using STAR. Quantify gene expression to generate count matrices. Normalize data with DESeq2 normalization or TPM to correct for sequencing depth and library size, then evaluate distribution consistency and adjust for batch effects if detected.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNASus scrofaAdelina Lopez Lopez JarafalseSuperovulation with eCG alone or combined with the GnRH analogue buserelin improves transferable embryo production in weaned sows without affecting embryo qualityThe objective of this study was to evaluate the effects of eCG administered alone or in combination with buserelin (BU) on ovulatory response, embryo production efficiency, developmental synchrony, and blastocyst transcriptomic profiles in weaned donor sows. The experiment comprised six trials, each conducted over a 1-week period with 8-14 sows. A total of 76 sows selected at weaning were randomly assigned to three experimental group: eCG group (n = 27); eCG + BU group (n = 29); and control group (n = 20). Sows in the eCG group received 1000 IU of equine chorionic gonadotropin (eCG, Folligon®, Intervet International B.V., Boxmeer, The Netherlands) 24 hours post-weaning to induce superovulation. Sows in the eCG + BU group received the same eCG treatment, followed by 10 µg of BU (2.5 mL Receptal®, Merck Sharp & Dohme Animal Health, S.L., Salamanca, Spain) at the onset of estrus. Control sows received no hormonal estimulation and were monitored for spontaneous estrus post-weaning. In vivo-developed embryos were surgically recovered on Day 6 after estrus. Four independent pools of 5 viable blastocysts per group (total n=20 blastocysts per group) were prepared for transcriptome analysis. Embryos were placed in sterile microcentrifuge tubes with 5 µL of PBS, immediately immersed in LN2 and stored at -80 °C until RNA extraction and subsequent RNA-seq analysis. After analysis, data were processed and normalized, and differentially expressed genes (DEGs) were identified for each hormonal treatment compared with the control. DEG lists were compared to identify treatment-specific gene expression changes. Pathway enrichment analysis was performed for each DEG list.2026-09-07T00:00:00Z2026-09-07T08:08:13.599Z2026-04-30T13:17:23.48ZE-MTAB-16983ERP192866E-MTAB-12820EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969