biostudies-arrayexpressMian FengEquus caballushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15170The development stage between two and three years old of age is very important for Thoroughbred horses, as the Thoroughbred horses would experience high intense exercise and training. This study was designed to investigate the transcriptional changes in the skeletal muscle of untrained Thoroughbred horses during this key transitional period.biostudies-arrayexpressLibrary Construction - RNA sequencing was conducted by the Research Technology Support Facility at Brigham Young University and the Research Technology Support Facility at Michigan State University. The TruSeq Stranded mRNA Library Preparation Kit LT (Illumina, San Diego, USA) was used to build the strand-specific and indexed Illumina sequencing libraries, which were pooled, with 18–20 indexed libraries per pool, and sequenced on an Illumina HiSeq 2500 platform using Rapid Run flow cells and reagents (Illumina).Sample Collection - Muscle samples were obtained from each horse standing at rest without sedation. Sample collection was performed between 7:30 am and 11:30 am, when all the horses were at rest. Approximately 300 mg muscle tissue was collected from the ventral compartment of the middle gluteal muscle (Valette et al. 1999). After collection, the muscle samples were stored in RNAlater (Thermo Fisher Scientific, Waltham, MA, USA) at 4°C for 24 hours and then transferred to a freezer at −20°C prior to RNA extraction.Nucleic Acid Extraction - RNA extraction, quantification and quality control (QC) was performed as previously described (Bryan et al. 2017; Farries et al. 2019). Briefly, approximately 70 mg of muscle tissue underwent nucleic acid extraction with TRIzol reagent (Thermo Fisher Scientific) followed by DNase (RNase free) treatment (Qiagen, Hilden, Germany).Sequencing - Each library pool was sequenced across both lanes of a flow cell through dual lane loading. Sequencing was performed using a 2 × 100 bp paired-end (PE100) method, after which the data were demultiplexed and converted to FASTQ format.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Differential gene expression analysis (UR3 vs. UR2) was performed using DEseq2 (v1.34.0) (Love et al. 2014). Covariates were incorporated to account for different sequencing pools, batches, and commercial providers. The normalization method is based on the DESeq2 software.Sequence Alignment - To ensure high-quality sequencing data and employing the Trim Galore (Felix Krueger et al. 2023) wrapper script, the Cutadapt (v.1.18) (Martin 2011) and FastQC (v.0.12.1) (Andrews 2010) software tools were used to trim adapter sequences and evaluate sequence read quality. The STAR aligner (v.2.7.10b) (Dobin et al. 2013) was then used to map sequence reads to the EquCab3 reference genome (Kalbfleisch et al. 2018). Following this, FeatureCounts (v.2.2.1) (Pertea et al. 2016) was used for transcript quantification in each sample.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500RNA-seq of coding RNAEquus caballusMian FengfalseRNA-seq of the ventral compartment of the middle gluteal muscle in untrained at resting Thoroughbred horses, comparing the age of two years old and three years oldThe development stage between two and three years old of age is very important for Thoroughbred horses, as the Thoroughbred horses would experience high intense exercise and training. This study was designed to investigate the transcriptional changes in the skeletal muscle of untrained Thoroughbred horses during this key transitional period.2026-05-20T00:00:00Z2026-05-20T01:01:30.012Z2025-05-28T14:47:35ZE-MTAB-15170ERP172985E-MTAB-5447EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184