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Prefrontal-raphe-habenular circuit drives fear memory recall and updating

GSE300145 Mus musculus (mouse) RNA-seq (gene expression) 38 samples Submitted 2026/06/30 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 38 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
38 samples: 38 × MRR,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; 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)
Fear memory recall is a vital defensive response, yet its underlying neuronal mechanism remains incompletely understood. Here, we identify a fear recall pathway. We found that hippocampal and amygdalar memory centers directly target a group of medial prefrontal cortex (mPFC) neurons, which are necessary for fear recall and directly target vesicular glutamate transporter 2 (vGluT2)-expressing neurons in the pontine median raphe region (MRRvGluT2 neurons) in mice.
Read the full summary ↓
We found that MRRvGluT2 neurons are necessary for recalling contextual and cued fear memories, they exhibit scalable fear-dependent activity, bidirectionally regulate depression-like behaviors, and show prolonged activity after a fearful experience. During fear memory recall, MRRvGluT2 neurons activate the lateral habenula (LHb), a region implicated in major depression. MRRvGluT2 neurons are electrophysiologically and genetically diverse, and present in rodent and primate species. The identified mPFC–MRR–LHb pathway critically mediates fear memory recall, providing potential therapeutic targets for fear-related disorders.
This dataset
Open GSE300145 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 GSE300145_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1279125 and SRA study SRP592940. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
38 × MRR,

Supports a between-group comparison across 38 samples.

How we read this: 1 replicated groups read from 38 sample titles; they account for 38 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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