GEO series

RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair

GSE303129 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 2 samples Submitted 2026/07/15 Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 2 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: 2 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.

Summary (written by the submitters)

DNA double-stranded breaks (DSBs) are an especially toxic form of damage that can be reversed without loss of genetic information by homology-directed repair (HDR), which copies from an intact template molecule. Finding a correct template within millions to billions of other DNA bases is termed homology search and is mediated by the protein RAD51.

Read the full summary ↓

A major challenge in understanding homology search is the lack of tools to monitor search itself, rather than the end-stage outcome of HDR. We developed RAD51 proximity identification sequencing (RaPID-seq), a highly sensitive in cellulo method that marks all DNA searched by RAD51, regardless of whether it is chosen as the final template. We find that HDR in human cells is hierarchical. Only DSB-proximal sequences are searched, and even identical sequences outside the proximal window are not efficiently interrogated. Final recombination is unlocked by template homology but only at proximal sequences. We further find that RAD51 efficiently searches exogenously introduced DNA templates, such as those commonly used during genome editing, even those with no homology to the DSB site. Such highly abundant exogenous templates compete with search of endogenous genome templates. Our data reveal the invisible process of homology search and shed new light on fundamental mechanisms underlying genome editing.

This dataset

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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 GSE303129_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 PRJNA1294220 and SRA study SRP602357. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

Datasets on a similar topic

GSE304074 RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair 118 samples shares rad51, double-stranded, constraints, proximity, homology, mapping, spatial, search
GSE303128 RAD51 proximity mapping reveals spatial constraints on homology search during DNA double-stranded break repair 8 samples shares rad51, double-stranded, constraints, proximity, homology, mapping, spatial, search
GSE217562 Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP ChIP] 16 samples shares proximity, mapping
GSE287088 Mapping the FOXA1 Interactome in ER+ Breast Cancer Cells using Proximity Labeling Reveals Novel Interactions with the Orphan Nuclear Receptor NR2C2 5 samples shares proximity, mapping
GSE311747 RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution [CLIP] 27 samples shares proximity, mapping
GSE299760 Mapping the FOXA1 Interactome in ER+ Breast Cancer Cells using Proximity Labeling Reveals Novel Interactions with the Orphan Nuclear Receptor NR2C2 [RNA-Seq] 12 samples shares proximity, mapping
GSE295471 in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes 8 samples shares proximity, mapping
GSE217563 Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ [ITS OMAP RIP] 6 samples shares proximity, mapping

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