Processed RNA‑seq outputs and SMASH morphometry (mFD) data for denervation remodeling across rat laryngeal and hindlimb muscles

This Figshare dataset contains the processed RNA‑seq outputs and morphometry summary files that support the manuscript “Denervation remodeling is graded by organ context and fiber subtype: integrated morphologic and transcriptomic analysis across rat laryngeal and hindlimb muscles.”Scope• Species & tissues: Sprague Dawley rat laryngeal muscles (medial thyroarytenoid, lateral thyroarytenoid, posterior cricoarytenoid) and hindlimb muscles (gastrocnemius, soleus).• Study design: Unilateral denervation (RLN transection for larynx; tibial nerve transection for hindlimb), 5‑week endpoint; contralateral side served as internal control.• Outputs included: morphometry (SMASH) mFD percent‑change tables by muscle/fiber subtype; RNA‑seq count matrices (raw and normalized) with gene annotations; DESeq2 result tables for injured vs. non‑injured comparisons in each tissue; curated ±4‑fold differential expression (DEG) CSVs; pathway heatmap exports for significantly enriched terms; Metascape GO heatmap CSVs; and study metadata.File inventory (representative file names)• Morphometry (SMASH mFD percent‑change CSVs):Gartling_MTA_IIX_SMASH_mFD Percent Change.csvGartling_LTA_IIB_SMASH_mFD Percent Change.csvGartling_PCA_IIA_SMASH_mFD Percent Change.csvGartling_Gastroc_IIX_SMASH_mFD Percent Change.csvGartling_Gastroc_IIB_SMASH_mFD Percent Change.csvGartling_SOLEUS_IIA_SMASH_mFD Percent Change.csvGartling_SOLEUS_MHC1_SMASH_mFD Percent Change.csv• RNA‑seq counts and annotations (TXT):Gartling_rnaseq_raw_counts_all_samples.txtGartling_rnaseq_raw_counts_with_annotations.txtGartling_rnaseq_normalized_counts_all_samples.txtGartling_rnaseq_normalized_counts_with_annotations.txt• DESeq2 results (TXT; per tissue injured vs. non‑injured):Gartling_DESeq2_results_gastrocnemius_injured_vs_noninjured.txtGartling_DESeq2_results_SOLEUS_injured_vs_noninjured.txtGartling_DESeq2_results_PCA_injured_vs_noninjured.txtGartling_DESeq2_results_MTA_injured_vs_noninjured.txtGartling_DESeq2_results_LTA_injured_vs_noninjured.txt• Curated ±4‑fold DEG tables (CSV):Gartling_Gastroc_DEG_4 Threshold.csvGartling_Soleus_DEG_4 Threshold.csvGartling_PCA_DEG_4 Threshold.csvGartling_MTA_DEG_4 Threshold.csvGartling_LTA_DEG_4 Threshold.csv• Pathway heatmap exports (CSV):Gastrocnemius: Oncostatin M; cytokine–cytokine receptor interaction; TGF‑β regulation of extracellular matrix; leptin influence on immune response:Gartling_Gastroc_Oncostatin M_heatmap.csvGartling_Gastroc_Cytokine-cytokine receptor interaction_Heatmap.csvGartling_Gastroc_TGF-beta regulation of extracellular matrix_Heatmap.csvGartling_Gastroc_Leptin influence on immune response_Heatmap.csvPCA: TP53 network:Gartling_PCA_TP53 Network_Heatmap.csv• GO term heatmap exports (CSV):Gartling_Upregulated_MetascapeHeatmapSelectedGO.csvGartling_Downregulated_MetascapeHeatmapSelectedGO.csv• Metadata (XLSX):Gartling_metadata.xlsxMethods summary (for context)• Morphometry: SMASH (Semi‑automatic Muscle Analysis using Segmentation of Histology) used on QuPath‑exported TIFFs; fiber types identified via MHC isoform immunolabeling; outcome metric = minimum Feret diameter (mFD) percent‑change denervated vs. control.• RNA‑seq processing: Trim/QA; alignment to rat genome (BN7.2); quantification; differential expression via DESeq2 with covariate correction by sex; pathway enrichment using BioPlanet 2019 and Metascape GO.