biostudies-arrayexpressDong Hyun SeoHomo sapiensbcl2fastq (Illumina)Illumina Experiment ManagerNot applicableStringTie v2.1.3b (for TPM calculation), R v4.3.2FastQC v0.11.7, Trimmomatic 0.38, HISAT2 v2.1.0, StringTie v2.1.3bhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15233Patients who underwent pre-operative thyroid ultrasound were retrospectively analyzed using radiomic profiling. A distinct radiomics-defined cluster (Cluster 2) was identified, and to investigate the underlying molecular alterations associated with this cluster, RNA sequencing was performed on samples with a high likelihood score for Cluster 2.biostudies-arrayexpressSample Collection - Patients with papillary thyroid carcinoma (PTC) underwent thyroidectomy at Yonsei Cancer Center or Yongin Severance Hospital. Resected tissues were snap-frozen in liquid nitrogen immediately and stored at –80 °C. Cytology was classified as Bethesda V/VI, and risk was stratified using ATA 2015 guidelines.Nucleic Acid Extraction - Total RNA was extracted using TRIzol® reagent (Invitrogen) per manufacturer's instructions. RNA concentration was measured using Quant-IT RiboGreen assay and quality evaluated using Agilent TapeStation. Only RNA with RIN ≥ 7.0 was used.Library Construction - RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit. mRNA was isolated with poly-T magnetic beads, fragmented, and converted to cDNA, followed by end repair, adapter ligation, and PCR enrichment.Sequencing - Indexed libraries were sequenced on an Illumina NovaSeq 6000 platform (2 × 100 bp paired-end). Raw reads were quality-checked with FastQC and trimmed using Trimmomatic.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Cleaned reads were aligned to GRCh37 (hg19) using HISAT2 v2.1.0. Transcript assembly was performed using StringTie v2.1.3b. Gene expression was quantified in FPKM and raw counts.Data Transformation - Gene expression data were normalized using TPM (Transcripts Per Million) to account for sequencing depth and gene length. For downstream analysis, log2 transformation of TPM values (log2[TPM + 1]) was applied to stabilize variance and approximate normal distribution.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsLiquid nitrogen freezer, surgical instrumentsIllumina NovaSeq 6000Benchtop centrifuge, vortex, NanoDrop or plate reader (for RiboGreen assay), TapeStation (Agilent)Thermal cycler (Bio-Rad C1000), Agilent 2100 Bioanalyzer, Qubit 4 FluorometerLinux server, HPC clusterRNA-seq of coding RNAHomo sapiensSunmi ParkJandee LeeDong Hyun SeoYoung Suk JofalseRNA seq of human thyroid cancer tissuePatients who underwent pre-operative thyroid ultrasound were retrospectively analyzed using radiomic profiling. A distinct radiomics-defined cluster (Cluster 2) was identified, and to investigate the underlying molecular alterations associated with this cluster, RNA sequencing was performed on samples with a high likelihood score for Cluster 2.2025-07-24T00:00:00Z2025-07-25T08:47:44.611Z2025-06-30T21:28:08.898ZE-MTAB-15233ERP174273EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184