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G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome [RNA-seq]

GSE283485 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2026/04/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 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
G-quadruplexes regulate chromatin accessibility and gene expression in Bloom SyndromebioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Bloom Syndrome (BS) is a recessive genetic disorder characterized by hyper-recombination and genome instability. It is caused by mutations in the conserved RecQ helicase gene, BLM, which acts to unwind various aberrant DNA structures. One such structure is DNA G-quadruplexes (G4s), which have broad regulatory functions. Despite previous association between putative G4-forming sequences and BS, it remains unclear what (dys)regulatory role, if any, endogenous G4 structures may play in BS.
Read the full summary ↓
Here, we profiled chromatin accessibility and gene expression via ATAC-seq and RNA-seq and mapped endogenous G4 via ChIP-seq in wild-type (WT) vs. BS cell lines. We observed that in BS, differential G4 formation positively correlated with both differential chromatin accessibility and gene expression. To test the direct involvement of G4s in the molecular phenotypes in BS, we applied pyridostatin, a G4-stabilizing molecule, in WT cells and showed that G4 stabilization partially phenocopied BS. Additionally, data from a BS family showed that regions with increased chromatin accessibility in BS individuals were also enriched for G4-forming sequences. Our data showed that G4 formation promotes chromatin accessibility and gene expression; likely in BS, unresolved G4 increases focal chromatin accessibility, thereby upregulating gene expression. In summary, our results revealed a central role of G4 in the molecular etiology of BS and provide a new perspective on BLM’s regulatory function through G4s.
Published in
G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome
Su D, Altmannova V, Soltys V et al. · bioRxiv : the preprint server for biology 2026 · PMID 41867784 · doi:10.64898/2026.03.03.709275
This dataset
Open GSE283485 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 GSE283485_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 PRJNA1194040 and SRA study SRP549336. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41867784) ↗
Study design
8 conditions, mostly in triplicate
GM16375, BLM-/-, none, RNAseq ×3 AG14980, Wildtype, none, RNAseq ×3 GM08505, BLM-/-, none, RNAseq ×3 GM00637, Wildtype, none, RNAseq ×3 AG14980, Wildtype, 0.4%DMSO for 24h, RNAseq ×3 AG14980, Wildtype, 10 µM PDS for 24h, RNAseq ×3 GM00637, Wildtype, 0.4%DMSO for 24h, RNAseq ×3 GM00637, Wildtype, 10 µM PDS for 24h, RNAseq ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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
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