GEO series

Cell cycle dynamics of chromosomal organisation at single-cell resolution

GSE94489 Mus musculus (mouse) Single-cell RNA-seq 49 samples Submitted 2017/07/06 Platform GPL17021Platform GPL16417Platform GPL15103Platform GPL19057

At a glance

Single-cell RNA-seq · mouse · 49 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 49 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Chromosomes in proliferating metazoan cells undergo dramatic structural metamorphoses every cell cycle, alternating between a highly condensed mitotic structure facilitating chromosome segregation, and a decondensed interphase structure accommodating transcription, gene silencing and DNA replication. These cyclical structural transformations have been evident under the microscope for over a century, but their molecular-level analysis is still lacking.

Read the full summary ↓

Here we use single-cell Hi-C to study chromosome conformations in thousands of individual cells, and discover a continuum of cis-interaction profiles that finely position individual cells along the cell cycle. We show that chromosomal compartments, topological domains (TADs), contact insulation and long-range loops, all defined by ensemble Hi-C maps, are governed by distinct cell cycle dynamics. In particular, DNA replication correlates with build-up of compartments and reduction in TAD insulation, while loops are generally stable from G1 through S and G2. Analysing whole genome 3D structural models using haploid cell data, we discover a radial architecture of chromosomal compartments with distinct epigenomic signatures. Our single-cell data creates an essential new paradigm for the re-interpretation of chromosome conformation maps through the prism of the cell cycle.

This dataset

Open GSE94489 in finder → Find more mouse datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE94489_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

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 PRJNA369960 and SRA study SRP098829. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28682332) ↗

Samples in this study

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

+ 49 more — browse all 49 samples with per-sample file links →

Datasets on a similar topic

GSE150817 Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution 30 samples shares single-cell, resolution, dynamics
GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares single-cell, resolution
GSE329967 Temporal Single-Cell Transcriptional Dynamics of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression 33 samples shares single-cell, dynamics
GSE310028 Dissecting Semaglutide-dependent transcriptome response in obesity and osteoarthritis across tissues at single-cell resolution 28 samples shares single-cell, resolution
GSE303460 Spatiotemporal single-cell atlas of suture stem cell dynamics in craniosynostosis [scRNA-Seq] 14 samples shares single-cell, dynamics
GSE266497 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [10x-v3-RNA-seq] 13 samples shares single-cell, resolution
GSE294795 Hypertension-Induced Neurovascular and Cognitive Dysfunction at Single-Cell Resolution 12 samples shares single-cell, resolution
GSE328655 A high-resolution, sex-stratified atlas of transcriptional and alternative splicing dynamics in the fasting mouse liver. 80 samples shares resolution, dynamics

Search all mouse datasets in GEO →

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.