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Transcriptomic changes in human SCC-25 Parental and RARG knockout cells in response to 6h and 48h treatments with RARγ agonists CD1530 or all-trans retinoic acid (RA).

GSE295225 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/12/12 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 conditions, mostly in triplicateGroups 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
Multiple modes of transcriptional regulation by the nuclear hormone receptor RARγ in human squamous cell carcinomaThe Journal of biological chemistry · 2026
Summary (written by the submitters)
Vitamin A (retinol) metabolism and signaling through nuclear retinoic acid receptors (RARs α,β,γ) regulate embryonic development, immune functions, and cell differentiation in most cell types. RAR gamma (RARγ) is highly expressed in stratified squamous epithelial cells of the tongue, esophagus, and skin. While data indicate that RARγ agonism is anti-tumorigenic in oral cavity squamous cell carcinoma (OCSCC), the specific, primary gene targets of RARγ remain poorly characterized.
Read the full summary ↓
Here, we define the transcriptomic consequences of RARγ activity in OCSCC. Using a CRISPR-Cas9-mediated knockout (KO) of RARγ and pharmacological treatments with RAR agonists, we identified RARγ-specific gene targets and pathways, as well as targets that overlap with other RA-responsive nuclear receptors.
Published in
Multiple modes of transcriptional regulation by the nuclear hormone receptor RARγ in human squamous cell carcinoma
Hoxie HR, Tang XH, Gudas LJ · The Journal of biological chemistry 2026 · PMID 41274504 · doi:10.1016/j.jbc.2025.110965
This dataset
Open GSE295225 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 GSE295225_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 PRJNA1253729 and SRA study SRP580258. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41274504) ↗
Study design
12 conditions, mostly in triplicate
SCC-25, PAR, Vehicle, 48h, ×3 SCC-25, RARG KO, Vehicle, 48h, ×3 SCC-25, PAR, 1μM CD1530, 48h, ×3 SCC-25, RARG KO, 1μM CD1530, 48h, ×3 SCC-25, PAR, 1μM Retinoic Acid, 48h, ×3 SCC-25, RARG KO, 1μM Retinoic Acid, 48h, ×3 SCC-25, PAR, Vehicle, 6h, ×3 SCC-25, RARG KO, Vehicle, 6h, ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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