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SOX9-BAF multi-omics profiling in human colon cancer cell models

GSE335210 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 173 samples Submitted 2026/06/16 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 173 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)
Topic
Colorectal cancerThis series is part of our curated briefing on it.
Samples
173 samples: 84 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.
Summary (written by the submitters)
This study combines matched ATAC-seq, RNA-seq, and CUT&RUN profiling in human colon cancer cell models to track SOX9 degradation/recovery, BAF subunit perturbation, histone-mark occupancy, ARID1A/ARID1B knockdown, and SOX9-variant chromatin accessibility. The main time-course series uses HT29-dTAG cells; the SOX9-variant ATAC-seq subset uses LS180 cells.
This dataset
Open GSE335210 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Colorectal 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 GSE335210_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 PRJNA1472915 and SRA study SRP705828. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
84 conditions, mostly in duplicate
Human matched ATAC-seq full time-course sampl… ×2 Human matched ATAC-seq full time-course sampl… ×2 Human matched ATAC-seq full time-course sampl… ×2 Human matched ATAC-seq full time-course sampl… ×2 Human matched ATAC-seq full time-course sampl… ×2 Human matched ATAC-seq full time-course sampl… ×2 Human ARID1A/ARID1B perturbation ATAC-seq sam… ×2 Human ARID1A/ARID1B perturbation ATAC-seq sam… ×2 +81 more

Supports a between-group comparison across 168 samples.

How we read this: 84 replicated groups read from 173 sample titles; they account for 168 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

+ 133 more — browse all 173 samples with per-sample file links →

More Colorectal cancer datasets

Search all human ChIP / ATAC / CUT&Tag 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.