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Analysis of ER stress-induced three-dimensional enhancer network in wild-type and transcription facotr-knockout HCT116 cells [RNA-Seq]

GSE324345 Homo sapiens (human) RNA-seq (gene expression) 66 samples Submitted 2026/07/01 Platform GPL24676Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 66 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
66 samples: 22 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
ATF4 and CHOP coordinate endoplasmic reticulum stress-responsive gene programs through enhancer activation and chromatin loopingNucleic acids research · 2026
Summary (written by the submitters)
Integrative analysis of transcriptome, enhancer landscape and transcription factor binding, and three-dimensional genome structure in wild-type and transcription factor-knockout cells folloowing tunicamycin treatment
Published in
ATF4 and CHOP coordinate endoplasmic reticulum stress-responsive gene programs through enhancer activation and chromatin looping
Joo JS, Kim M, Kim S et al. · Nucleic acids research 2026 · PMID 42333810 · doi:10.1093/nar/gkag641
This dataset
Open GSE324345 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 GSE324345_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 PRJNA1434446 and SRA study SRP682324. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42333810) ↗
Study design
22 conditions, mostly in triplicate
WT_Con_RNA_SET1 ×3 WT_Tm_RNA_SET1 ×3 WT_Con_RNA_SET2 ×3 WT_Tm_RNA_SET2 ×3 ATF4_KO_Con_RNA_SET2 ×3 ATF4_KO_Tm_RNA_SET2 ×3 ATF6_KO_Con_RNA_SET2 ×3 ATF6_KO_Tm_RNA_SET2 ×3 +14 more

Supports a between-group comparison across 66 samples.

How we read this: 22 replicated groups read from 66 sample titles; they account for 66 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

+ 26 more — browse all 66 samples with per-sample file links →

Datasets on a similar topic

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.