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Gene regulatory landscape dissected by single-cell four-omics sequencing

GSE303006 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2026/01/18 Platform GPL34290
At a glance

Single-cell RNA-seq · mouse · 16 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
16 samples: 3 × mouse brain RNA modality, vs 3 × mouse brain Accessibility modality, vs 3 × mouse brain HiC modality, vs 3 × mouse brain H3K27ac histone modification,Groups 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.
Summary (written by the submitters)
Enrichment libraries and Hi-C libraries were processed using identical scripts. Initially, different read types were demultiplexed based on identification sequences in the R2 read. For RNA data, we first removed reads containing no poly-A sequence following GAT5-RT primer sequence. We then aligned Read 1 to the GRCm38 reference genome using STAR.
Read the full summary ↓
Duplicates were removed based on UMIs with UMI-tools. RNA count matrix was generated by FeatureCounts with parameters “-O -M --fraction”. We used RNAsnpSplit for phasing of allele- specific RNA counts.For HiC data, reads were mapped to the GRCm38 reference genome with BWA-mem2 in “5SP” mode. Contacts and 3D genome structures were generated with Hickit software using default parameters. To remove potential contamination from RNA reads, we cleaned contacts between two exons from the same transcript, which accounted for ~0.04% of all contacts. For quality control of reconstructed 3D genome structures, five replicates were generated with random seeds, and median RMSD for each combination of 3 replicates was calculated. The first replicate in the combination with the minimum median RMSD value (if < 1.5) was used for downstream analysis. 3D proximity and 3D distance maps were generated as previously described with custom codes. For accessibility reads and histone modification reads, R2 reads, which represent Tn5 insertion sites, were aligned using BWA-mem2 with default parameters. Afterward, a custom Python script was employed to remove PCR duplicates, generating single-cell signal fragment files. For haplotype phasing, fragments were first assigned to a haplotype using SNP information from the R2 read. If the haplotype could not be determined from R2, SNP information from the R1 read was then utilized. All reads were mapped to the mm10 reference genome. All these processing steps were organized and implemented using Snakemake, and are available at https://github.com/skelviper/CHARM.
This dataset
Open GSE303006 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 (GSE303006_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 PRJNA1284811. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × mouse brain RNA modality, vs 3 × mouse brain Accessibility modality, vs 3 × mouse brain HiC modality, vs 3 × mouse brain H3K27ac histone modification,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 12 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
Datasets on a similar topic

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