biostudies-arrayexpressDong Hyun SeoHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15264This study aimed to investigate the distinct molecular characteristics of atypical thyroid cancer in comparison to follicular adenoma and widely invasive follicular thyroid carcinoma (wiFTC). Tumor tissues from three patients with atypical thyroid cancer were collected during the same surgical period, alongside control samples from three individuals diagnosed with either follicular adenoma or wiFTC. All RNA samples used for downstream transcriptomic analysis had RNA integrity numbers (RIN) greater than 7.0, ensuring high-quality input for sequencing.biostudies-arrayexpressSample Treatment - This is not applicable to the present study, as it is a retrospective analysis of human clinical samples.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.Sample Collection - Patients with papillary thyroid carcinoma (PTC) underwent thyroidectomy at Yonsei Cancer Center. 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.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.Growth Protocol - This is not applicable to the present study, as it is a retrospective analysis of human clinical samples.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.UnknownTranscriptomicsGenomicsProteomicsNot applicable in this studyLiquid 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 sequencing data of follicular adenoma, widely invasive follicular thyroid carcinoma and atypical thyroid cancerThis study aimed to investigate the distinct molecular characteristics of atypical thyroid cancer in comparison to follicular adenoma and widely invasive follicular thyroid carcinoma (wiFTC). Tumor tissues from three patients with atypical thyroid cancer were collected during the same surgical period, alongside control samples from three individuals diagnosed with either follicular adenoma or wiFTC. All RNA samples used for downstream transcriptomic analysis had RNA integrity numbers (RIN) greater than 7.0, ensuring high-quality input for sequencing.2026-05-20T00:00:00Z2026-05-20T05:56:26.439Z2025-06-25T13:56:22.366ZE-MTAB-15264ERP174032EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969