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High-throughput exploration of single-cell transcriptional alterations associated with remote fear memory formation

GSE254380 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2025/01/01 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 18 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
18 samples: 5 × Fear conditioned cerebral single cell RNASeq vs 5 × Home caged cerebellar single cell RNASeq vs 4 × Fear conditioned cerebellar single cell RNASeq vs 4 × Home caged cerebral single cell RNASeqGroups 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)
Leveraging SPEED in tandem with snRNA-Seq, we uncover molecular identities of distinct neural subtypes, concurrent 5hmC alterations at active enhancers and gene bodies, and dynamic gene expression associated with remote memory formation. This comprehensive analysis encompasses several thousand cells from the cerebral and cerebellar cortex of home-caged (HC) and fear-conditioned (FC) mice.
This dataset
Open GSE254380 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 GSE254380_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 PRJNA1070279 and SRA study SRP486382. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × Fear conditioned cerebral single cell RNASeq vs 5 × Home caged cerebellar single cell RNASeq vs 4 × Fear conditioned cerebellar single cell RNASeq vs 4 × Home caged cerebral single cell RNASeq

Supports a between-group comparison across 18 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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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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.