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APE1-Mediated Transcriptional Reprogramming in Esophageal Adenocarcinoma Cells under Acidic Bile Reflux Stress

GSE342322 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2026/08/06 Platform GPL24676
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)
Topic
Esophageal cancerThis series is part of our curated briefing on it.
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.
Summary (written by the submitters)
Esophageal adenocarcinoma (EAC) arises in the setting of Barrett's esophagus, an intestinal metaplastic precursor lesion that can develop in patients with chronic Gastroesophageal reflux disease (GERD). This study investigates the genome-wide transcriptional adaptations and molecular stress responses mediated by Apurinic/apyrimidinic endonuclease 1 (APE1) in EAC cells under reflux-induced stress.
Read the full summary ↓
By utilizing APE1 genetic silencing alongside exposure to an acidic bile salt (ABS), this dataset defines the global differential gene expression profiles, altered signaling pathways, and transcriptional networks that depend on APE1 for survival during reflux stress.
This dataset
Open GSE342322 in finder → Find more human RNA-seq datasets → Esophageal 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 GSE342322_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 PRJNA1507370 and SRA study SRP724097. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
FLO1-shControl ×3 FLO1-shControl-ABS ×3 FLO1-shAPE1#1 ×3 FLO1-shAPE1#1-ABS ×3 FLO1-shAPE1#3 ×3 FLO1-shAPE1#3-ABS ×3 OE33-shControl ×3 OE33-shContorl-ABS ×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
More Esophageal cancer datasets

Search all human RNA-seq datasets in GEO →

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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.