GEO series
Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [ATAC-Seq]
GSE320163
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
377 samples
Submitted 2026/02/26
Platform GPL34281Platform GPL28330Platform GPL29480Platform GPL34328
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 377 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
- 377 samples: 128 conditions, mostly in triplicateGroups 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
- Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identityCell stem cell · 2026
Summary (written by the submitters)
While CRISPR/Cas9 holds therapeutic promise, broader application demands understanding complications in vast non-coding regions. We found that CRISPR/Cas9 can cause premature differentiation of neural stem cells in vivo and mouse embryonic stem cells in vitro, even when cleavage occurred at distant sites tens of kilobases away from the nearest regulatory elements.
Read the full summary ↓
To investigate this, we employed an integrated ATAC/RNA approach (AR-seq) and identified editing-induced chromatin accessibility change, with its scale varying by cell types. Cells with stemness are most affected, experiencing perturbations that extend over a hundred kilobases. Furthermore, even local DNA perturbations can disrupt CTCF- and condensate-associated chromatin architecture, causing distal transcriptional rewiring and ultimately loss of stemness identity. To minimize chromatin perturbations and preserve cell identity we refined gene editing strategies, including distance-aware sgRNA design, pharmacological attenuation of DNA resection, and alternative editing systems. This work paves the way for safer and broader application of genome editing technologies.
Published in
Zhu M, Yuan J, Meng Q et al.
· Cell stem cell 2026
· PMID 41742419
· doi:10.1016/j.stem.2026.01.015
This dataset
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.
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 GSE320163_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1426988 and SRA study SRP678683. Searching any of these in the dataset finder brings you back here.
Study design
128 conditions, mostly in triplicate
ATAC-seq 20201013_nih3t3_cas9_wt ×6
ATAC-seq 20210218_hek293t_be_EMX1 ×6
ATAC-seq 20210218_hek293t_be_TYR ×6
ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna ×3
ATAC-seq 20200928_hek293t_cas9_EMX1 ×3
ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna ×3
ATAC-seq 20200928_hek293t_cas9_TYR ×3
ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sg… ×3
+120 more
Supports a between-group comparison across 377 samples.
How we read this: 128 replicated groups read from 377 sample titles; they account for 377 of them. 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
- GSM9536288 ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep1 ATAC-seq 20200928_hek29…
- GSM9536289 ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep2 ATAC-seq 20200928_hek29…
- GSM9536290 ATAC-seq 20200928_hek293t_cas9_EMX1_dead_sgrna_rep3 ATAC-seq 20200928_hek29…
- GSM9536291 ATAC-seq 20200928_hek293t_cas9_EMX1_rep1 ATAC-seq 20200928_hek29…
- GSM9536292 ATAC-seq 20200928_hek293t_cas9_EMX1_rep2 ATAC-seq 20200928_hek29…
- GSM9536293 ATAC-seq 20200928_hek293t_cas9_EMX1_rep3 ATAC-seq 20200928_hek29…
- GSM9536294 ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep1 ATAC-seq 20200928_hek29…
- GSM9536295 ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep2 ATAC-seq 20200928_hek29…
- GSM9536296 ATAC-seq 20200928_hek293t_cas9_TYR_dead_sgrna_rep3 ATAC-seq 20200928_hek29…
- GSM9536297 ATAC-seq 20200928_hek293t_cas9_TYR_rep1 ATAC-seq 20200928_hek29…
- GSM9536298 ATAC-seq 20200928_hek293t_cas9_TYR_rep2 ATAC-seq 20200928_hek29…
- GSM9536299 ATAC-seq 20200928_hek293t_cas9_TYR_rep3 ATAC-seq 20200928_hek29…
- GSM9536300 ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep1 ATAC-seq 20200928_hek29…
- GSM9536301 ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep2 ATAC-seq 20200928_hek29…
- GSM9536302 ATAC-seq 20200928_hek293t_cas9_ZSWIM3_dead_sgrna_rep3 ATAC-seq 20200928_hek29…
- GSM9536303 ATAC-seq 20200928_hek293t_cas9_ZSWIM3_rep1 ATAC-seq 20200928_hek29…
- GSM9536304 ATAC-seq 20200928_hek293t_cas9_ZSWIM3_rep2 ATAC-seq 20200928_hek29…
- GSM9536305 ATAC-seq 20200928_hek293t_cas9_ZSWIM3_rep3 ATAC-seq 20200928_hek29…
- GSM9536306 ATAC-seq 20200928_hek293t_cas9_cas9_only_vector_rep1 ATAC-seq 20200928_hek29…
- GSM9536307 ATAC-seq 20200928_hek293t_cas9_cas9_only_vector_rep2 ATAC-seq 20200928_hek29…
- GSM9536308 ATAC-seq 20200928_hek293t_cas9_cas9_only_vector_rep3 ATAC-seq 20200928_hek29…
- GSM9536309 ATAC-seq 20200928_hek293t_cas9_empty_vector_rep1 ATAC-seq 20200928_hek29…
- GSM9536310 ATAC-seq 20200928_hek293t_cas9_empty_vector_rep2 ATAC-seq 20200928_hek29…
- GSM9536311 ATAC-seq 20200928_hek293t_cas9_empty_vector_rep3 ATAC-seq 20200928_hek29…
- GSM9536312 ATAC-seq 20200928_hek293t_cas9_wt_rep1 ATAC-seq 20200928_hek29…
- GSM9536313 ATAC-seq 20200928_hek293t_cas9_wt_rep2 ATAC-seq 20200928_hek29…
- GSM9536314 ATAC-seq 20200928_hek293t_cas9_wt_rep3 ATAC-seq 20200928_hek29…
- GSM9536315 ATAC-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep1 ATAC-seq 20201013_nih3t…
- GSM9536316 ATAC-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep2 ATAC-seq 20201013_nih3t…
- GSM9536317 ATAC-seq 20201013_nih3t3_cas9_EMX1_dead_sgrna_rep3 ATAC-seq 20201013_nih3t…
- GSM9536318 ATAC-seq 20201013_nih3t3_cas9_EMX1_rep1 ATAC-seq 20201013_nih3t…
- GSM9536319 ATAC-seq 20201013_nih3t3_cas9_EMX1_rep2 ATAC-seq 20201013_nih3t…
- GSM9536320 ATAC-seq 20201013_nih3t3_cas9_EMX1_rep3 ATAC-seq 20201013_nih3t…
- GSM9536321 ATAC-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep1 ATAC-seq 20201013_nih3t…
- GSM9536322 ATAC-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep2 ATAC-seq 20201013_nih3t…
- GSM9536323 ATAC-seq 20201013_nih3t3_cas9_TYR_dead_sgrna_rep3 ATAC-seq 20201013_nih3t…
- GSM9536324 ATAC-seq 20201013_nih3t3_cas9_TYR_rep1 ATAC-seq 20201013_nih3t…
- GSM9536325 ATAC-seq 20201013_nih3t3_cas9_TYR_rep2 ATAC-seq 20201013_nih3t…
- GSM9536326 ATAC-seq 20201013_nih3t3_cas9_TYR_rep3 ATAC-seq 20201013_nih3t…
- GSM9536327 ATAC-seq 20201013_nih3t3_cas9_ZSWIM3_dead_sgrna_rep1 ATAC-seq 20201013_nih3t…
+ 337 more — browse all 377 samples with per-sample file links →
Datasets on a similar topic
- GSE320165 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [Cut&Tag] 46 samples shares far-extending, perturbation, minimizing, chromatin, preserves, identity, editing
- GSE320162 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [RNA-Seq] 347 samples shares far-extending, perturbation, minimizing, chromatin, preserves, identity, editing
- GSE338103 Linker histone H1.0 and JUNB Interaction Maintains Lineage-Specific and Age-Dependent Chromatin Architecture to Safeguard Cell Identity [ATAC-seq] 14 samples shares chromatin, identity, atac-seq
- GSE65360 Single-cell chromatin accessibility data using scATAC-seq 1632 samples shares chromatin, atac-seq
- GSE225993 Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [ATAC-seq] 16 samples shares chromatin, atac-seq
- GSE273644 HDAC6 Inhibition Disrupts HDAC6-P300 Interaction Reshaping the Cancer Chromatin Landscape (ATAC-Seq) 12 samples shares chromatin, atac-seq
- GSE67446 Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing [ATAC-seq] 6 samples shares chromatin, atac-seq
- GSE292571 SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [ChIP-seq] 116 samples shares chromatin
Share this dataset
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.