Damascus goat mammary gland transcriptome under mixed and artificial rearing systems: 3’ mRNA-seq gene count matrix, sample metadata, and differential expression results

Abstract

This dataset contains processed 3’ mRNA sequencing data generated from mammary gland epithelial biopsies of second-lactation Damascus goats under two rearing systems: artificial rearing (AR) and mixed rearing (MR). Kids in the AR group were weaned 48h post partum while in the MR group were allowed to suckle on their mother for seven weeks. In both groups does were machine milked twice daily. Mammary gland tissue biopsies were collected at 42 days postpartum (n = 6 per treatment group). Libraries were prepared from total RNA using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) and sequenced on an Illumina MiSeq platform (150-cycle kit). Raw reads were quality-checked using FastQC (v0.12.1) and processed with Cutadapt (v4.4) to remove adapters, poly(A) tails, and low-quality bases. Reads were aligned to the Capra hircus reference genome assembly ARS1.2 using STAR aligner (v2.7.10b). Gene-level counts were generated using the quantMode option in STAR. Because libraries were sequenced across multiple runs, batch effects were corrected using ComBat-seq. Differential expression analysis was performed using DESeq2 (v1.40.2). Genes with adjusted P-value < 0.05 were considered differentially expressed; adjusted P-value < 0.1 indicated a trend for differential expression. The Excel file includes five sheets: -Supplemental Table 1: Transcriptomic analysis pipeline output in number of reads per library. -Supplemental Table 2: Gene Ontology Terms' attributes of the differentially expressed genes for GO domains Molecular Function, Biological process and Cellular Component. -gene_count_table: raw gene counts per library, prior to differential expression analysis. -sample_metadata: library identifiers, treatment group (AR or MR) and sequencing batch. -Full_DE_results: complete DESeq2 output including baseMean, log2FoldChange (lfc), lfc Standard Error (lfcSE), Wald statistic (stat), P-value, and adjusted P-value. These data support the findings reported in Sfakianaki et al., Journal of Dairy Science, 2026, Kid suckling versus artificial rearing: Effects in Damascus goat milk production parameters and the mammary gland transcriptome. https://doi.org/10.3168/jds.2026-28481