Tracking-seq reveals the heterogeneity of off-target effects in CRISPR/Cas9-mediated genome editing
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 111 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
- 111 samples: 97 distinct titles, 14 of them repeatedGroups 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
- Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editingNature biotechnology · 2025
Read the full summary ↓
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 GSE236360_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 PRJNA990699 and SRA study SRP447116. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 111 sample titles: 97 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.
- GSM8124403 ABE HEK1 12h HEK293T 400k PEI rep1
- GSM8124404 ABE HEK1 24h HEK293T 400k PEI rep1-2
- GSM8124405 ABE HEK1 24h HEK293T 400k PEI rep1
- GSM8124406 ABE HEK1 48h HEK293T 400k PEI rep1
- GSM8124407 ABE HEK1 72h HEK293T 400k PEI rep1
- GSM8124408 ABE HEK4 12h HEK293T 500k PEI rep1
- GSM8124409 ABE HEK4 24h HEK293T 500k PEI rep1-2
- GSM8124410 ABE HEK4 24h HEK293T 500k PEI rep1
- GSM8124411 ABE HEK4 48h HEK293T 500k PEI rep1
- GSM8124412 ABE HEK4 72h HEK293T 500k PEI rep1
- GSM8124413 ABE VEGFA3 24h HEK293T 500k PEI rep1
- GSM8124414 ABE VEGFA3 24h HEK293T 500k PEI rep2
- GSM8124415 CBE-dCas9 HEK4 24h HEK293T 500k PEI rep1
- GSM8124416 CBE-dCas9 HEK4 24h HEK293T 500k PEI rep2
- GSM8124417 CBE HEK4 12h HEK293T 500k PEI rep1
- GSM8124418 CBE HEK4 24h HEK293T 500k PEI rep1-2
- GSM8124419 CBE HEK4 24h HEK293T 500k PEI rep1
- GSM8124420 CBE HEK4 36h HEK293T 500k PEI rep1
- GSM8124421 CBE HEK4 48h HEK293T 500k PEI rep1
- GSM8124422 CBE VEGFA2 12h HEK293T 500k PEI rep1
- GSM8124423 CBE VEGFA2 24h HEK293T 500k PEI rep1
- GSM8124424 CBE VEGFA2 36h HEK293T 500k PEI rep1
- GSM8124425 CBE VEGFA2 48h HEK293T 500k PEI rep1
- GSM8124426 Cas9 FANCF 96h HEK293T 500k PEI rep1
- GSM8124427 Cas9 HEK1 96h HEK293T 400k PEI rep1
- GSM8124428 Cas9 HEK3 96h HEK293T 500k PEI rep1
- GSM8124429 Cas9 HEK3 96h HEK293T 500k PEI rep2
- GSM8124430 Cas9 HEK4 12h HEK293T 500k PEI rep1
- GSM8124431 Cas9 HEK4 24h HEK293T 500k PEI rep1
- GSM8124432 Cas9 HEK4 48h HEK293T 500k ELEC-noFACS-RNP
- GSM8124433 Cas9 HEK4 48h HEK293T 500k ELEC-noFACS-plasmid
- GSM8124434 Cas9 HEK4 48h HEK293T 500k ELEC rep1
- GSM8124435 Cas9 HEK4 48h HEK293T 500k PEI rep1
- GSM8124436 Cas9 HEK4 48h HEK293T 500k with-dsDNAase
- GSM8124437 Cas9 HEK4 48h HEK293T 500k without-dsDNAase
- GSM8124438 Cas9 HEK4 72h HEK293T 500k PEI rep1
- GSM8124439 Cas9 HEK4 96h HEK293T 500k PEI batch1
- GSM8124440 Cas9 HEK4 96h HEK293T 500k PEI batch2-1
- GSM8124441 Cas9 HEK4 96h HEK293T 500k PEI batch2-2
- GSM8124442 Cas9 HEK4 96h HEK293T 500k PEI rep1
+ 71 more — browse all 111 samples with per-sample file links →
- GSE92872 Pooled CRISPR screening with single-cell transcriptome read-out 100 samples shares crispr
- GSE293920 Programmable RNA acetylation with CRISPR-Cas13 56 samples shares crispr
- GSE54745 Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells 18 samples shares crispr
- GSE272457 Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER [scRNA-seq] 16 samples shares crispr
- GSE245463 Prediction and validation of a human immunodeficiency with CRISPR 14 samples shares crispr
- GSE281868 Identification of epigenetic regulators of fibrotic transformation in cardiac fibroblasts through bulk and single-cell CRISPR screens (ATAC-Seq_2) 12 samples shares crispr
- GSE335904 In Vivo CRISPR Screens Identify SLC1A5 as a Metabolic Checkpoint for Cancer Immunotherapy [ATAC] 4 samples shares crispr
- GSE277747 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling 1 samples shares crispr
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.