Supporting data for "Dietary brown mushroom stem reshapes the cecal microbiome and mucosal immune response of layer chicks"

This dataset provides supporting data for the study “Dietary brown mushroom stem reshapes the cecal microbiome and mucosal immune response of layer chicks.” The study evaluated dietary brown mushroom stem (BMS) across four treatment groups: Control (0% BMS), T1 (2% BMS), T2 (4% BMS), and T3 (6% BMS). Immune gene expression was measured in ileal mucosa using RT-qPCR, and the microbiome data were obtained from cecal contents. The deposit includes technical Ct measurements, relative-expression values, sample metadata, and a data dictionary for eight immune genes: IL1B, IL6, TNF-alpha, IFN-gamma, TLR4, IL10, TGFB1, and IL4. The RT-qPCR dataset contains 40 samples, of which 39 have matching microbiome records in the supplied dataset. Additional files include genus-level relative-abundance and count matrices, taxonomic annotations, gene–genus correlation results, distance-based redundancy analysis (db-RDA/CAP) output tables, five-fold cross-validated neural-network performance results, and the matched gene-expression matrix used for the integrated analyses. ASV-level BIOM tables, representative ASV sequences, and a QIIME2 feature-table artifact are also included. Raw 16S rRNA gene amplicon sequencing reads are deposited separately in the NCBI Sequence Read Archive under BioProject accession PRJNA1504972 and are not duplicated in this deposit. The README file describes the deposited files, treatment coding, sample matching, and data-processing information.