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Genome-wide DNA replication profiling and full-length total RNA sequencing from the same single cell

GSE278959 Homo sapiens (human) Single-cell RNA-seq 546 samples Submitted 2025/08/26 Platform GPL20795Platform GPL21273Platform GPL34284
At a glance

Single-cell RNA-seq · human · 546 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
546 samples: 25 conditions, mostly in duplicateGroups 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
scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phaseNature communications · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase
Poonperm R, Yoneda T, Imada T et al. · Nature communications 2025 · PMID 41397953 · doi:10.1038/s41467-025-64688-1
This dataset
Open GSE278959 in finder → Find more 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 GSE278959_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 PRJNA1169828 and SRA study SRP536989. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41397953) ↗
Study design
25 conditions, mostly in duplicate
RNA_CBMS1_scRR1_WholeS ×49 DNA_CBMS1_scRR1_WholeS ×49 RNA_CBMS1_scRR3_WholeS ×35 DNA_CBMS1_scRR3_WholeS ×35 RNA_HAP1_scRR1_MidS ×31 RNA_RPE1_scRR1_Lot2_WholeS ×24 DNA_RPE1_scRR1_Lot2_WholeS ×24 RNA_RPE1_scRamDA_MidS ×15 +43 more

Supports a between-group comparison across 374 samples.

How we read this: 25 replicated groups read from the first 400 of 546 sample titles; they account for 374 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

+ 506 more — browse all 546 samples with per-sample file links →

Datasets on a similar topic

Search all RNA-seq 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.