Replication Fork-Associated RNA-DNA Hybrids Safeguard Genomic Stability in Transcriptionally Active Regions
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 87 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
- 87 samples
- 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
- DDX39A resolves replication fork-associated RNA-DNA hybrids to balance fork protection and cleavage for genomic stability maintenanceMolecular cell · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE254536_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1070985 and SRA study SRP545418. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 87 more — browse all 87 samples with per-sample file links →
- GSE240664 RNA-DNA hybrids formed in the absence of Senataxin drive non-coding RNA expression and protein aggregation in the nucleolus 17 samples shares rna-dna, hybrids
- GSE275821 TOP2B cooperates with ATRX to resolve G-quadruplexes and maintain replication fork stability in glioma 12 samples shares replication, stability
- GSE292952 NAT10-mediated β-hydroxybutyrylation Facilitates DNA Replication, Reduces Replication Stress and Genomic Instability 12 samples shares replication, stability
- GSE220073 Dynamics of de novo heterochromatin assembly and disassembly at replication forks ensures fork stability 12 samples shares replication, stability
- GSE252173 Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A. 42 samples shares rna-dna
- GSE252171 Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A [RNA-seq] 36 samples shares rna-dna
- GSE281129 Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer 794 samples shares replication
- GSE306391 G-Quadruplex DNA suppresses Transcription during DNA Replication [CUT&Tag] 264 samples shares replication
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.