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The Role of Epithelial IKKβ in the Transition from Normal to Precancerous Tissue in Esophageal Epithelium

GSE294269 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/09/01 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 16 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
Mus musculus (mouse)
Samples
16 samples: 5 × control, 4-NQO, pai vs 5 × IKKβ knockout, 4-NQO, pai vs 3 × control, vehicle, pai vs 3 × IKKβ knockout, vehicle, paiGroups 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.
Summary (written by the submitters)
Esophageal cancer is the 6th leading cause of cancer related death with a 5-year survival rate of under 20%. Esophageal squamous cell carcinoma (ESCC) is associated with chronic inflammation and injury. Currently, little is understood about the molecular mechanisms regulating the early stages of esophageal carcinogenesis. The NFB/IKK pathway plays a central role in inflammation and has been implicated in ESCC.
Read the full summary ↓
However, its functional role in the transition to esophageal precancer is unknown. To investigate this, we utilized ED-L2/Cre mice to knockout IKKβ (IKKβEEC-KO) in the esophagus. These mice and littermate controls were treated with the carcinogen 4-nitroquinoline-1-oxide (4-NQO) or a vehicle for one month. Esophagi were harvested and examined through histological, protein, flow cytometry, and RNA analyses. Histological analysis showed that 4-NQO treatment led to increased inflammation and intraepithelial CD45+ immune cells which was largely attenuated in IKKβEEC-KO mice. Total T cells, Tregs, CD4+, and CD8+ T cells showed a similar trend, while macrophages showed a reverse trend. RNAseq data showed upregulation of inflammatory pathways and downregulation in wound healing related pathways in 4-NQO treated control mice versus knockout. We also saw increased expression of the chemokine CXCL9, a T cell chemoattractant. This increase was blocked in 4-NQO treated IKKβEEC-KO mice or in mice treated with anti-IFN. Additionally, we demonstrated in vitro that IFN upregulates CXCL9 in a NF-ĸB dependent manner in esophageal keratinocytes. So epithelial IKK regulates the immune landscape in the transition to precancer through IFN/CXCL9 signaling and recruitment of T cells to the esophagus.
This dataset
Open GSE294269 in finder → Find more mouse 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 GSE294269_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 PRJNA1248913 and SRA study SRP578154. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × control, 4-NQO, pai vs 5 × IKKβ knockout, 4-NQO, pai vs 3 × control, vehicle, pai vs 3 × IKKβ knockout, vehicle, pai

Supports a case/control comparison: 5 samples read as cases, 8 as controls.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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
Datasets on a similar topic

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