biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsAgata Wilktranscription profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16876With increasing detection of thyroid nodules due to the widespread availability of sonography, and the subjective nature of cytological assessment, molecular evaluation can support physicians in distinguishing benign and malignant nodules. The dataset consists of 20 benign or malignant biopsy samples, and includes gene expression measured using the high-density microarray Human Transcriptome 2.0 (Affymetrix) and associated metadata. The samples are categorised according to the Bethesda System for Reporting Thyroid Cytopathology. The samples include cases where the aspiration did not puncture the nodule, which is indicated in the sample info.biostudies-arrayexpressNucleic Acid Extraction - RNA isolation was performed using RNA RNeasy Micro (Qiagen, GmbH, Hilden, Germany) in accordance with the protocol by the manufacturer.Labeling - The concentration of the obtained RNA was measured using a Qubit microfluorimeter (Thermofisher) using the Quant-iT RNA Assay Kit reagent dedicated to assess the concentration of ribonucleotide acid. 10 nanograms of total RNA from each sample were used to prepare biotinylated fragmented cRNA using GeneChip® Wt Pico reagent Kit according to Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays Use Guide, P/N 703262.Hybridization - Gene expression was assessed using GeneChip® Human Genome (HTA) 2.0 microarrays (Affymetrix, now ThermoFisher). Hybridization was perform according the manufacturer’s protocol, GeneChip® Expression Wash, Stain and Scan User Guide for Cartridge Arrays, P/N 702731. Arrays were washed and stained using the Fluidics Station 450.Sample Collection - Samples were collected during ultrasound-guided fine-needle aspiration biopsy of thyroid nodules qualified for biopsy into Eppendorf tubes containing 200 µl of RNAprotect Cell Reagent buffer or 350 μl of RLT buffer and then frozen at [-80]°C. External biopsies, due to transport, were placed in Cell Reagent buffer and biopsies were collected in place for RLT buffer. The biopsy needle, attached to a syringe, was gently rinsed with the buffer from the tube and frozen at -80 Celsius degrees.Scaning - Arrays were scanned using the GeneChip® Scanner 3000 7G according the manufacturer’s protocol, GeneChip® Expression Wash, Stain and Scan User Guide for Cartridge Arrays, P/N 702731. The quality analysis of the microarrays was carried out in the \"Transcriptome Analysis Console\", version 4.0, using the SST-RMA standardisation.MIAME ScoreRaw DataOrganizationAssays and DataMAGE-TAB FilesArray DesignsDagmara RusinekEwa StobieckaEwa Zembala-NożyńskaJolanta KrajewskaKrzysztof FujarewiczMagdalena KołtonDaria Handkiewicz-JunakMałgorzata Oczko-WojciechowskaMichał JarząbAgata WilkBarbara JarząbAndrzej MarszałekElwira Bakuła-ZalewskaSebastian StudentMarek DedecjusEwa ChmielikKrzysztof ŁakomiecAgnieszka CzarnieckaKrzysztof KaliszewskiAgnieszka Kotecka-BlicharzAleksandra PfeiferMonika HalczokTomasz TyszkiewiczDorota Słowińska-KlenckaAlicja PłuciennikfalseMicroarray gene expression profiling of fine needle aspiration biopsy of thyroid nodules in Polish patientsWith increasing detection of thyroid nodules due to the widespread availability of sonography, and the subjective nature of cytological assessment, molecular evaluation can support physicians in distinguishing benign and malignant nodules. The dataset consists of 20 benign or malignant biopsy samples, and includes gene expression measured using the high-density microarray Human Transcriptome 2.0 (Affymetrix) and associated metadata. The samples are categorised according to the Bethesda System for Reporting Thyroid Cytopathology. The samples include cases where the aspiration did not puncture the nodule, which is indicated in the sample info.2026-04-15T00:00:00Z2026-04-15T15:32:37.037Z2026-04-09T08:33:05.139ZE-MTAB-16876E-MTAB-15380EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003815