← BioTransfer GEO Dataset Finder
GEO series

FN1 Shapes the Behavior of Papillary Thyroid Carcinoma through Alternative Splicing of EDB Region

GSE285016 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/01/08 Platform GPL29480
At a glance

RNA-seq (gene expression) · human · 10 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)
Topic
Thyroid cancerThis series is part of our curated briefing on it.
Samples
10 samples: 5 conditions, mostly in duplicateGroups 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
FN1 shapes the behavior of papillary thyroid carcinoma through alternative splicing of EDB regionScientific reports · 2025
Summary (written by the submitters)
Papillary thyroid cancer (PTC) is often characterized by the indolent behavior with slow cell proliferation, however, small tumors still have a tendency to metastasize to the cervical lymph node, and the molecular mechanisms underlying that remain poorly understood. FN1 is an extracellular matrix (ECM) protein with the controversial role in tumors, containing three alternative splicing domains.
Read the full summary ↓
In this study, FN1 was as the hottest gene of PTC and distinctive expression in PTC cells. The alternatively splicing EDB region of FN1 was exclusively expressed in tumors, which impacted on integrin β1 (ITGB1) bonding FN1 and it secretion process, resulting in completely distinct roles of two isoforms of FN1 including and skipping EDB domain. EDB(-)FN1 intracellularly inhibited tumor proliferation, whereas extracellular EDB(+)FN1 activated migration, invasion and lymphoangiogenesis in vitro and in vivo. Mechanistically, EDB(-)FN1 upregulated p21 in p53 signaling pathway, however, EDB(+)FN1 secretes into ECM promoted VEGFC expression. Collectively, FN1 is a potential determinant behind the characteristic behavior of PTC with its two isoforms playing distinct roles owing to the alternative splicing of EDB domain.
Published in
FN1 shapes the behavior of papillary thyroid carcinoma through alternative splicing of EDB region
Liu M, Chen P, Wei B et al. · Scientific reports 2025 · PMID 39747903 · doi:10.1038/s41598-024-83369-5
This dataset
Open GSE285016 in finder → Find more human RNA-seq datasets → Thyroid cancer landscape →
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 GSE285016_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 PRJNA1200810 and SRA study SRP552843. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39747903) ↗
Study design
5 conditions, mostly in duplicate
shControl ×2 shFN1 ×2 OE-EDB(+)FN1 ×2 OE-EDB(-)FN1 ×2 shZMAT3 ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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
More Thyroid cancer datasets

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.