GEO series

Loss of ATM causes R-loop-associated transcriptional dysregulation and attenuates the related response to DNA damage [RNA-Seq]

GSE304101 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/02/18 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 18 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: Loss of ATM causes R-loop-associated transcriptional dysregulation and attenuates the related response to DNA damageThe Journal of biological chemistry · 2026

Summary (written by the submitters)

An early childhood onset neurodegenerative disorder, Ataxia Telangiectasia (AT) affects 1 in 40,000 to 100,000 individuals worldwide and is caused by mutations in the ataxia telangiectasia mutated (ATM) threonine-serine kinase, which regulates the DNA damage response (DDR). While the cause of AT has been known for years, the exact molecular mechanisms underlying disease progression, particularly at the transcriptomic level, remain poorly understood.

Read the full summary ↓

Three stranded structures, known as R-loops, have recently emerged as important players in the DDR via regulating key gene expression. Here, we utilized neuronal progenitor cells (NPCs) derived from induced pluripotent stem cells reprogrammed from patient-derived somatic cells to identify how loss of ATM impacts R-loop and transcriptional dynamics, both at baseline and in response to acute DNA damage. AT-derived NPCs (AT-NPCs) exhibited elevated spontaneous R-loop levels compared to controls (C-NPCs), as well as a strong positive correlation between R-loop accumulation and gene expression on a subset of dysregulated genes. Upon acute damage, loss of ATM resulted in an attenuated response, characterized by the impaired R-loop and transcriptional response to irradiation. Both C- and AT-NPCs underwent a similar cell cycle arrest, but AT-NPCs displayed an attenuated R-loop and transcriptional response, failing to activate proper DDR response. Importantly, R-loop formation is required for many key genes to properly respond to DNA damage, supporting a direct and causal role in this process. Overall, our data reveal an underappreciated mechanistic link between ATM, R-loop regulation, and transcription, the disruption of which may contribute to the impaired DDR observed in AT-NPCs.

Published in

Loss of ATM causes R-loop-associated transcriptional dysregulation and attenuates the related response to DNA damage

Westover KR, Hou Y, Wang F et al. · The Journal of biological chemistry 2026 · PMID 41544707 · doi:10.1016/j.jbc.2026.111161

This dataset

Open GSE304101 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 GSE304101_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 PRJNA1298912 and SRA study SRP604681. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41544707) ↗

Study design

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

Supports a case/control comparison: 3 samples read as cases, 6 as controls.

How we read this: Read from 18 sample titles: 18 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

GSM9143406 GM03487 cells, ATM null, no treatment
GSM9143407 GM08436 cells, ATM null, no treatment
GSM9143408 GM01526 cells, ATM null, no treatment
GSM9143409 425 cells, control, no treatment
GSM9143410 426 cells, control, no treatment
GSM9143411 427 cells, control, no treatment
GSM9143412 GM03487 cells, ATM null, irradiation
GSM9143413 GM08436 cells, ATM null, irradiation
GSM9143414 GM01526 cells, ATM null, irradiation
GSM9143415 425 cells, control, irradiation
GSM9143416 426 cells, control, irradiation
GSM9143417 427 cells, control, irradiation
GSM9386698 GM01526 cells, ATM null, RNaseH1 overexpression, irradiated
GSM9386699 GM03487 cells, ATM null, RNaseH1 overexpression, irradiated
GSM9386700 GM08436 cells, ATM null, RNaseH1 overexpression, irradiated
GSM9386701 425 cells, control, RNaseH1 overexpression, irradiated
GSM9386702 426 cellls, control, RNaseH1 overexpression, irradiated
GSM9386703 427 cells, control, RNaseH1 overexpression, irradiated

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