{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dong Hyun Seo"],"organism":["Homo sapiens"],"software":["bcl2fastq (Illumina)","Illumina Experiment Manager","Not applicable","StringTie v2.1.3b (for TPM calculation), R v4.3.2","FastQC v0.11.7, Trimmomatic 0.38, HISAT2 v2.1.0, StringTie v2.1.3b"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15233"],"description":["Patients 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Liquid nitrogen freezer, surgical instruments","Illumina NovaSeq 6000","Benchtop centrifuge, vortex, NanoDrop or plate reader (for RiboGreen assay), TapeStation (Agilent)","Thermal cycler (Bio-Rad C1000), Agilent 2100 Bioanalyzer, Qubit 4 Fluorometer","Linux server, HPC cluster"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Sunmi Park","Jandee Lee","Dong Hyun Seo","Young Suk Jo"],"additional_accession":[]},"is_claimable":false,"name":"RNA seq of human thyroid cancer tissue","description":"Patients 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.","dates":{"release":"2025-07-24T00:00:00Z","modification":"2025-07-25T08:47:44.611Z","creation":"2025-06-30T21:28:08.898Z"},"accession":"E-MTAB-15233","cross_references":{"ENA":["ERP174273"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}