biostudies-arrayexpressGertraud OrendMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16360Tumor-draining lymph nodes (TdLNs) were collected from wild-type (WT) and tenascin-C knockout (TNC-KO) C57BL/6 mice (N = 3 per group), each bearing 4NQO-induced tongue tumors. Both male and female mice were included. Beginning at 12 weeks of age, mice were exposed to 4NQO via drinking water for 16 weeks. Tumors were then subjected to a single 2 Gy irradiation. TdLNs were harvested six weeks after irradiation, and total RNA was isolated for bulk RNA-seq analysis.biostudies-arrayexpressSample Collection - 4-NQO was administered to 8 weeks old WT and TNCKO mice, which had been backcrossed with C57BL/6J mice for over 10 generations. The compound was delivered through drinking water at a final concentration of 100 μg/ml for 16 weeks. Following this treatment, the mice received a single 2 Gy dose of photon irradiation under anesthesia . After irradiation, the animals were provided with regular water for 6 weeks prior to sacrifice. At the time of euthanasia, tongue and mandibular lymph nodes (Tumor draining Lymph Nodes (TdLNs) were harvested.Library Construction - RNA-seq libraries were prepared using NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep Kit Illumina kits.Sequencing - Paired end sequencing (2x100bp) was performed on a Nextseq2000 (Illumina) using XLEAP-SBS reagents.Nucleic Acid Extraction - Total RNA was extracted from lymph node samples using the Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA quality and concentration were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer 2100. Only samples with RNA Integrity Number (RIN) ≥ 8 were used for library preparation and downstream RNA-seq analysis.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw RNA-seq reads were trimmed using Trimmomatic v0.39, aligned to the reference genome using STAR v2.7.10, and counts generated with featureCounts. Counts were normalized using DESeq2 (v1.40.0) variance-stabilizing transformation. Lowly expressed genes (counts < 10) were filtered out.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep Kit Illumina kitsIllumina HiSeq 2000RNA-seq of coding RNAMus musculusGertraud OrendNuohan WANGfalseRNA seq of tumor draining lymph node (TdLNs) from a wildtype (WT) or tenascin-C (TNC) knockout (KO) mouse each bearing 4NQO-carcinogen induced tongue tumorsTumor-draining lymph nodes (TdLNs) were collected from wild-type (WT) and tenascin-C knockout (TNC-KO) C57BL/6 mice (N = 3 per group), each bearing 4NQO-induced tongue tumors. Both male and female mice were included. Beginning at 12 weeks of age, mice were exposed to 4NQO via drinking water for 16 weeks. Tumors were then subjected to a single 2 Gy irradiation. TdLNs were harvested six weeks after irradiation, and total RNA was isolated for bulk RNA-seq analysis.2025-12-11T00:00:00Z2026-05-27T17:32:56.008Z2025-12-02T22:57:28.708ZE-MTAB-16360ERP185987EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184