RNA-seq dataset of fresh and cryopreserved sperm from Girolando (Bos taurus × Bos indicus) bulls
Description
This dataset contains processed RNA-seq data from fresh and cryopreserved sperm of two Girolando (Bos taurus × Bos indicus) bulls. The supplementary files include raw and TMM-normalized gene-count matrices, consensus significant genes identified using DESeq2 and edgeR, and bibliographic annotations of genes previously linked to sperm function, cryosurvival, cryotolerance, or fertility. A higher number of consensus significant genes was identified in comparisons between fresh and cryopreserved sperm than between the two cryopreservation treatments. Given that only two bulls were included, the differential transcript-abundance results are considered exploratory. The data may serve as a reference for comparative transcriptomic analyses and future studies on sperm cryotolerance and fertility-related traits specifically in cryopreserved sperm.
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Steps to reproduce
Fresh semen was collected from two sexually mature Girolando (Bos taurus × Bos indicus) bulls and divided into untreated fresh sperm and two cryopreservation treatments: manual vapor-phase freezing (Treatment A) and programmable freezing (Treatment B), both adapted from a USDA bull semen cryopreservation protocol. Spermatozoa were purified before total RNA extraction using the PrimeWay Total RNA Extraction Kit, followed by RNA quality assessment and preparation for sequencing. Libraries were prepared using the TruSeq Stranded Total RNA kit and sequenced as paired-end reads on an Illumina NovaSeq 6000. Raw reads were quality-filtered using fastp v0.23.2 and summarized with MultiQC v1.6. Filtered reads were aligned to the Bos taurus reference genome GCA_002263795.3 using HISAT2 v2.2.1, and gene-level counts were generated using HTSeq v0.11.3. Raw counts were also normalized using the trimmed mean of M-values (TMM) method. Differential transcript abundance was assessed using DESeq2 and edgeR, with consensus significant genes defined from results meeting the specified significance and fold-change criteria in both methods. Genome-guided transcriptome assemblies were generated using Trinity and assessed with BUSCO v5.8.2 using the mammalian lineage dataset.
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Funders
- Department of Agriculture-Bureau of Agricultural Research (DA-BAR)Grant ID: DA-BAR-2023-0008
- Department of Agriculture-National Livestock Program (DA-NLP)Grant ID: DA-BAR-2025-04-00051