GEO series

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_2]

GSE267126 Mus musculus (mouse) Single-cell RNA-seq 80 samples Submitted 2025/08/30 Platform GPL28457

At a glance

Single-cell RNA-seq · mouse · 80 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: 80 samples: 6 conditions, mostly with about 25 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.

Summary (written by the submitters)

The three-dimensional (3D) organization of cis-regulatory elements (CREs) plays a central role in transcription control. However, capturing transcriptome, epigenome, and 3D genome from the same single cells remains technically challenging. Here, we present scHiCAR (single-cell Hi-C with ATAC and RNA-seq), a combinatorial barcoding-based method that simultaneously profiles mRNA, open chromatin, and chromosome-conformation-capture from the same cells.

Read the full summary ↓

Compared to existing single-cell 3D genome methods, scHiCAR more efficiently enriches long-range cis-interactions anchored at candidate CREs (cCREs). Applied to 1.62 million mouse brain cells and complemented with a deep learning-based loop caller, scHiCAR accurately defines cell-type-specific transcriptomes, accessible cCREs, and 5kb-resolution enhancer-promoter pairs across 22 brain cell types. scHiCAR also performs robustly in challenging tissues such as skeletal muscle, enabling tri-modal single-cell level analysis of gene regulation dynamics during muscle stem cell regeneration. scHiCAR offers a scalable, efficient, and cost-effective platform for studying gene regulatory landscapes in complex tissues at single-cell resolution.

This dataset

Open GSE267126 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 GSE267126_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 PRJNA1109822 and SRA study SRP506926. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 25 replicates each

frontal cortex, RNA, batch3, ×25 frontal cortex, DNA, batch3, ×25 frontal cortex, RNA, batch2, ×11 frontal cortex, DNA, batch2, ×11 frontal cortex, RNA, batch1, ×3 frontal cortex, DNA, batch1, ×3 frontal cortex, RNA, batch4, ×1 frontal cortex, DNA, batch4, ×1

Supports a between-group comparison across 78 samples.

How we read this: 6 replicated groups read from 80 sample titles; they account for 78 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

GSM8260394 frontal cortex, RNA, batch3, rep1 frontal cortex, RNA, ba…
GSM8260395 frontal cortex, RNA, batch3, rep2 frontal cortex, RNA, ba…
GSM8260396 frontal cortex, RNA, batch3, rep3 frontal cortex, RNA, ba…
GSM8260397 frontal cortex, RNA, batch3, rep4 frontal cortex, RNA, ba…
GSM8260398 frontal cortex, RNA, batch3, rep5 frontal cortex, RNA, ba…
GSM8260399 frontal cortex, RNA, batch3, rep6 frontal cortex, RNA, ba…
GSM8260400 frontal cortex, RNA, batch3, rep7 frontal cortex, RNA, ba…
GSM8260401 frontal cortex, RNA, batch3, rep8 frontal cortex, RNA, ba…
GSM8260402 frontal cortex, RNA, batch3, rep9 frontal cortex, RNA, ba…
GSM8260403 frontal cortex, RNA, batch3, rep10 frontal cortex, RNA, ba…
GSM8260404 frontal cortex, RNA, batch3, rep11 frontal cortex, RNA, ba…
GSM8260405 frontal cortex, RNA, batch3, rep12 frontal cortex, RNA, ba…
GSM8260406 frontal cortex, RNA, batch3, rep13 frontal cortex, RNA, ba…
GSM8260407 frontal cortex, RNA, batch3, rep14 frontal cortex, RNA, ba…
GSM8260408 frontal cortex, RNA, batch3, rep15 frontal cortex, RNA, ba…
GSM8260409 frontal cortex, RNA, batch3, rep16 frontal cortex, RNA, ba…
GSM8260410 frontal cortex, RNA, batch3, rep17 frontal cortex, RNA, ba…
GSM8260411 frontal cortex, RNA, batch3, rep18 frontal cortex, RNA, ba…
GSM8260412 frontal cortex, RNA, batch3, rep19 frontal cortex, RNA, ba…
GSM8260413 frontal cortex, RNA, batch3, rep20 frontal cortex, RNA, ba…
GSM8260414 frontal cortex, RNA, batch3, rep21 frontal cortex, RNA, ba…
GSM8260415 frontal cortex, RNA, batch3, rep22 frontal cortex, RNA, ba…
GSM8260416 frontal cortex, RNA, batch3, rep23 frontal cortex, RNA, ba…
GSM8260417 frontal cortex, RNA, batch3, rep24 frontal cortex, RNA, ba…
GSM8260418 frontal cortex, RNA, batch3, rep25 frontal cortex, RNA, ba…
GSM8260419 frontal cortex, RNA, batch4, rep26
GSM8260420 frontal cortex, RNA, batch2, rep27 frontal cortex, RNA, ba…
GSM8260421 frontal cortex, RNA, batch2, rep28 frontal cortex, RNA, ba…
GSM8260422 frontal cortex, RNA, batch1, rep29 frontal cortex, RNA, ba…
GSM8260423 frontal cortex, RNA, batch1, rep30 frontal cortex, RNA, ba…
GSM8260424 frontal cortex, RNA, batch1, rep31 frontal cortex, RNA, ba…
GSM8260425 frontal cortex, RNA, batch2, rep32 frontal cortex, RNA, ba…
GSM8260426 frontal cortex, RNA, batch2, rep33 frontal cortex, RNA, ba…
GSM8260427 frontal cortex, RNA, batch2, rep34 frontal cortex, RNA, ba…
GSM8260428 frontal cortex, RNA, batch2, rep35 frontal cortex, RNA, ba…
GSM8260429 frontal cortex, RNA, batch2, rep36 frontal cortex, RNA, ba…
GSM8260430 frontal cortex, RNA, batch2, rep37 frontal cortex, RNA, ba…
GSM8260431 frontal cortex, RNA, batch2, rep38 frontal cortex, RNA, ba…
GSM8260432 frontal cortex, RNA, batch2, rep39 frontal cortex, RNA, ba…
GSM8260433 frontal cortex, RNA, batch2, rep40 frontal cortex, RNA, ba…

+ 40 more — browse all 80 samples with per-sample file links →

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Search all mouse RNA-seq datasets in GEO →

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