DOI: 10.6084/m9.figshare.30880157
title: Processed RNA‑seq outputs and SMASH morphometry (mFD) data for denervation remodeling across rat laryngeal and hindlimb muscles

description: his 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.”<br>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.<br>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<br>• 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<br>• 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<br>• 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<br>• 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<br>• GO term heatmap exports (CSV):Gartling_Upregulated_MetascapeHeatmapSelectedGO.csvGartling_Downregulated_MetascapeHeatmapSelectedGO.csv<br>• Metadata (XLSX):Gartling_metadata.xlsx<br>Methods 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.