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Ultra-resolution, multiscale live imaging reveals TADs as domains of cohesin-accelerated search

GSE289566 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2026/01/28 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 13 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
13 samples: 13 samples, each with a distinct title — no replicated groupsGroups 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
RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imagingScience (New York, N.Y.) · 2025
Summary (written by the submitters)
In the last decade, sequencing methods like Hi-C have made it clear the genome is intricately folded, (e.g. in TADs, stripes and dots), and that this organization contributes significantly to the control of gene expression and thence cell fate and behavior. Single-cell DNA tracing microscopy and polymer physics-based simulations of genome folding, have proposed these population-scale patterns arise from motor-driven, heterogeneous movement, rather than stable 3D genomic architecture, implying that motion, rather than structure, is key to understanding genome function.
Read the full summary ↓
However tools to directly observe this motion in vivo have been limited in coverage and resolution. Here, we introduce TRansposon Assisted Chromatin Kinetic Imaging Technology (TRACK-IT), which combines a suite of imaging and labeling improvements to achieve ultra-resolution in space and time, with self-mapping transposons to distribute labels across the chromosome. We find, in the presence of cohesin, that elements at submegabase separation exhibit search times as fast as a few to few tens of seconds - faster than the sampling interval of most recent studies. Acute degradation of cohesin leads to longer search times and a stronger dependence of search time on the linear separation at submegabase scales, but minimal change at multimegabase scales. Loci separated by a TAD border exhibited increased search times compared to distance matched controls. Finally, cohesin containing cells exhibited rare, processive movements, not seen in cohesin depleted cells. These processive trajectories exhibit extrusion rates of four kb/s across three distinct genomic intervals, four fold faster than recent in vitro measurements. Taken together, these results reveal a genome in constant motion on the seconds timescale, where motor dependent extrusion produces TADs that manifest as kinetic domains of accelerated local search.
Published in
RETRACTED: Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Lee J, Chen LF, Gaudin S et al. · Science (New York, N.Y.) 2025 · PMID 40966347 · doi:10.1126/science.adx2202
This dataset
Open GSE289566 in finder → Find more mouse RNA-seq datasets →
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 GSE289566_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1223449 and SRA study SRP563858. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40966347) ↗
Study design
13 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 13 sample titles: 13 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.

Samples in this study
Datasets on a similar topic

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