Data from: Repurposing clinically safe drugs for DNA repair pathway choice in CRISPR genome editing and synthetic lethality
Data files
Jun 19, 2026 version files 21.34 GB
Abstract
This dataset contains sequencing and immunoblot data from human cells treated with FDA-approved drugs to assess effects on double-strand DNA break repair pathways (NHEJ, MMEJ, HDR). The data include mutational outcomes and protein expression changes in key repair factors, supporting identification of drugs that modulate DNA repair for therapeutic applications.
Associated publication:
Macak, D., Kanis, P. & Riesenberg, S. Repurposing clinically safe drugs for DNA repair pathway choice in CRISPR genome editing and synthetic lethality. Nat Commun 16, 11077 (2025).
https://doi.org/10.1038/s41467-025-67243-0
Overview
This dataset contains all next-generation sequencing (NGS) data and raw immunoblot images generated from CRISPR-edited target sites in human cell cultures, as reported in the above publication. DNA repair pathway choice was assessed following drug or genetic perturbation in human cell lines.
Sequencing data were obtained by Illumina MiSeq 2×150 bp paired-end sequencing of genomic DNA amplicons spanning CRISPR target sites. Immunoblot data were obtained from protein extracts of human cell lines. For detailed experimental methods, please refer to the original publication.
Data Organization
All data are contained within a single ZIP archive:
Sequencing_and_Immunoblot_Data_For_Repurposing_Clinically_Safe_Drugs.zip
Files are organized into subfolders corresponding to individual figures and figure panels of the publication. All subfolders contain Illumina .bam files, except Fig_4_Immunoblots_Raw, which contains raw .tif immunoblot images and an Excel summary table.
File Naming Convention
BAM files follow this naming scheme:
Cell-line/gRNAtarget_replicate
For example: out.409B2_NOVA1_cytarabine_rep1.bam
Specific identifiers (IDs; e.g., A1198) refer to the drugs of the DiscoveryProbe FDA-Approved Drug Library (ApexBio, catalog no. L1021, as of November 2, 2021). For the full list, please refer to Supplementary Data 1 of the original publication.
Subfolder Structure
Sequencing_and_Immunoblot_Data_For_Repurposing_Clinically_Safe_Drugs.zip
│
├── Fig_1/
│ ├── H2O_controls/
│ ├── EtOH_controls/
│ └── DMSO_controls/
├── Fig_2b/
├── Fig_2d/
├── Fig_2e/
├── Fig_3a/
├── Fig_3b/
├── Fig_3c/
├── Fig_3e_Suppl_Fig_12/
├── Fig_3f/
├── Fig_3g/
├── Fig_3h/
├── Fig_5_Immunoblots_Raw/
├── Fig_5g/
│
├── Suppl_Fig_5/
├── Suppl_Fig_6/
├── Suppl_Fig_7/
├── Suppl_Fig_8b/
├── Suppl_Fig_8c/
├── Suppl_Fig_10/
└── Suppl_Fig_13/
Figure Descriptions
| Folder(s) | Figure | Description |
|---|---|---|
Fig_1/ |
Fig. 1 | Drug screening for DSB repair pathway modulators |
Fig_2b/, Fig_2d/, Fig_2e/ |
Fig. 2 | Characterization of repurposed DSB repair modulator drugs |
Fig_3a/–Fig_3h/, Fig_3e_Suppl_Fig_12/ |
Fig. 3 | Novel protein modulators of DSB repair pathways |
| (see Fig. 3 folders) | Fig. 4 | Mechanistic insights of ESR2 and AOX1 in DSB repair |
Fig_5_Immunoblots_Raw/, Fig_5g/ |
Fig. 5 | Synthetic lethality by drugs repurposed as DSB repair pathway outcome inhibitors |
Suppl_Fig_5/–Suppl_Fig_13/ |
Supplementary Figs. 5–13 | Supplementary data supporting main figures |
File Types
| File type | Description | Location |
|---|---|---|
.bam |
Illumina paired-end sequencing alignments | All folders except Fig_5_Immunoblots_Raw/ |
.tif |
Raw immunoblot images | Fig_5_Immunoblots_Raw/ |
.xlsx |
Summary table of immunoblot quantifications | Fig_5_Immunoblots_Raw/ |
Sharing / Access
This dataset is shared under the terms specified by Dryad. Please cite the original publication when using these data: Macak, D., Kanis, P. & Riesenberg, S. Repurposing clinically safe drugs for DNA repair pathway choice in CRISPR genome editing and synthetic lethality. Nat Commun 16, 11077 (2025). https://doi.org/10.1038/s41467-025-67243-0
Code / Software
No custom analysis code is deposited here. For information on the data analysis, please refer to the Methods section of the original publication.