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Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR

GSE305889 Homo sapiens (human) Single-cell RNA-seq 177 samples Submitted 2025/08/30 Platform GPL28457Platform GPL31277
At a glance

Single-cell RNA-seq · human · 177 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
177 samples: 23 conditions, mostly with about 5 replicates eachGroups 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
Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCARNature biotechnology · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR
Wei X, Xu Y, Yang D et al. · Nature biotechnology 2026 · PMID 41714417 · doi:10.1038/s41587-026-03013-7
This dataset
Open GSE305889 in finder → Find more 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 GSE305889_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 PRJNA1308126 and SRA study SRP506778. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41714417) ↗
Study design
23 conditions, mostly with about 5 replicates each
human H1, GM12878 and mouse ESC, DNA, batch1, ×32 frontal cortex, RNA, batch3, ×25 frontal cortex, DNA, batch3, ×25 frontal cortex, RNA, batch2, ×11 frontal cortex, DNA, batch2, ×11 mouse Pvalb neuron, ×5 mouse mucle, BaCl2 injure, day0, RNA, biolog… ×5 mouse mucle, BaCl2 injure, day5, RNA, biolog… ×5 +17 more

Supports a between-group comparison across 175 samples.

How we read this: 23 replicated groups read from 177 sample titles; they account for 175 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

+ 137 more — browse all 177 samples with per-sample file links →

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