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Dysregulation of Vitamin D and Its Signaling in Hashimoto's Thyroiditis in Korean Population

GSE286332 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2025/09/01 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
18 samples: 9 × Thyroid, PTC without HT vs 9 × Thyroid, PTC with HTGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Dysregulated vitamin D signaling in Hashimoto's thyroiditis: an integrated transcriptomic study in a Korean cohortFrontiers in endocrinology · 2025
Summary (written by the submitters)
Hahimoto’s thyroiditis (HT) is the most common thyroid disease leads to hypothyroid in developed countries. Recent studies highlighted the Vitamin D as the potential risk factor or the therapeutic agents for the HT due to its role in modulating immune responses, while the concrete evidence has not been presented. Patients eligible for the surgery of papillary thyroid cancer (PTC) with or without HT were recruited for the study.
Read the full summary ↓
We analyzed serum thyroid biomarkers including serum vitamin D, anti-TG, anti-TPO for HT patients. Using the RNA-seq the gene expression profile of thyroid tissue, potential correlation between HT and vitamin D or its signaling was investigated. HT cohort showed common clinical characteristics known for the HT in serum biomarkers and enrichment analysis of BP terms and KEGG pathways. Serum vitamin D level was significantly lower in HT patients. However, vitamin D receptor (VDR) expression and genes involved in vitamin D-associated BP terms were significantly upregulated in HT. Real-time PCR and Immunofluorescence staining confirmed enhanced VDR expression throughout the thyroid tissue of HT cohort. This study demonstrated dysregulated vitamin D signaling in thyroid tissue of HT cohort. Further study need to be performed to elucidate etiology, susceptibility, and development of HT in relation with vitamin D signaling.
Published in
Dysregulated vitamin D signaling in Hashimoto's thyroiditis: an integrated transcriptomic study in a Korean cohort
Lim DW, Jeong HJ, Lee JS et al. · Frontiers in endocrinology 2025 · PMID 41113708 · doi:10.3389/fendo.2025.1666115
This dataset
Open GSE286332 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE286332_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1208932 and SRA study SRP556453. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41113708) ↗
Study design
9 × Thyroid, PTC without HT vs 9 × Thyroid, PTC with HT

Supports a between-group comparison across 18 samples.

How we read this: 2 replicated groups read from 18 sample titles; they account for 18 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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