GEO series

Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ATAC-seq]

GSE308846 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 6 samples Submitted 2026/08/06 Platform GPL18573

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 6 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 6 samples: 6 samples, each with a distinct title — no replicated groupsGroups 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: Reprogramming lineage features promotes epithelial behavior in carcinoma cellsCancer letters · 2026

Summary (written by the submitters)

Cancer cells distort epigenetic control of gene expression, allowing for a remarkable degree of plasticity and loss of cell type identity. At the same time, expression of identity-discordant lineage determinants can significantly shift cell phenotype by creating lineage hybrid states. One example is the misexpression of IKZF3, encoding the lymphocyte restricted transcription factor Aiolos, by roughly half of non-small cell lung carcinomas (NSCLC) and the majority of small cell lung carcinomas [1].

Read the full summary ↓

During normal lymphocyte development, pre-B progenitors enter a proliferative phase dependent on survival cues from bone marrow stroma. To progress, Aiolos and its paralog Ikaros (IKZF1) repress multiple adhesion-related genes, releasing cells from this epithelial-type dependence on solid matrix in preparation for their release as mature lymphocytes into the circulation [2, 3]. In lung cancers, unlicensed expression of Aiolos initiates a similar shift from an epithelial to a lymphocyte-like state by repression of multiple adhesion-related genes, resulting in loss of anoikis and consequent metastatic spread [1]. To reverse these lymphoid traits, we created a chimeric epigenetic editor designed to specifically retrieve Aiolos-repressed epithelial adhesion properties. Here, we demonstrate proof of principle for epithelial lineage restoration by exploiting a lymphocyte developmental pathway.

Published in

Reprogramming lineage features promotes epithelial behavior in carcinoma cells

Wu RF, Fu G, Liao C et al. · Cancer letters 2026 · PMID 41192784 · doi:10.1016/j.canlet.2025.218117

This dataset

Open GSE308846 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE308846_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1332806 and SRA study SRP625285. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41192784) ↗

Study design

6 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 6 sample titles: 6 distinct titles with little repetition. 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

GSM9253916 control bio rep 1, ATAC
GSM9253917 control bio rep 2, ATAC
GSM9253918 control bio rep 3, ATAC
GSM9253919 TA bio rep 1, ATAC
GSM9253920 TA bio rep 2, ATAC
GSM9253921 TA bio rep 3, ATAC

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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.