GEO series

Projection-defined amygdala neurons encode emotional memory through distinct transcriptomic programs

GSE316516 Mus musculus (mouse) Single-cell RNA-seq 15 samples Submitted 2026/01/19 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 15 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 15 samples: 5 conditions, mostly in triplicateGroups 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 amygdala is crucial for emotional memory, but the molecular programs that enable its distinct circuits to encode different memory features remain unclear. Combining single-cell RNA sequencing with retrograde tracing, we investigated transcriptomic dynamics of amygdala neurons projecting to nucleus accumbens (NAc) or auditory/temporal association cortex (AuC/TeA) during formation and long-term retention of fear and reward memories.

Read the full summary ↓

We found that memory engages pathway-specific transcriptional programs of synaptic genes determined by valence, temporal stage, and projection target. Notably, the AMY→AuC/TeA pathway, previously considered a fear circuit, showed robust modulation during reward memory retention, and chemogenetic silencing confirmed its essential role in reward memory. Projection-defined neurons are transcriptionally and functionally heterogeneous: some subpopulations encode a single feature of emotional memory, such as an AMY→NAc subpopulation for reward memory formation and retention, and an AMY→AuC/TeA subpopulation for retention of fear and reward memories. Most subpopulations, however, encode multiple features via largely non-overlapping gene programs. We further identified Dcn as a selective marker for an AMY→NAc subpopulation preferentially recruited during fear memory formation. Our findings reveal a principle of projection-, valence-, and time-dependent transcriptional programming, demonstrate how subpopulations multiplex memory features via dynamic gene networks, and provide a comprehensive resource for dissecting amygdala function.

This dataset

Open GSE316516 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 GSE316516_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 PRJNA1403048 and SRA study SRP662446. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 conditions, mostly in triplicate

Mouse brain, Control, ×3 Mouse brain, Fc2h, ×3 Mouse brain, Fc5d, ×3 Mouse brain, Rc2h, ×3 Mouse brain, Rc5d, ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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

GSM9455131 Mouse brain, Control, rep1 Mouse brain, Control,
GSM9455132 Mouse brain, Control, rep2 Mouse brain, Control,
GSM9455133 Mouse brain, Control, rep3 Mouse brain, Control,
GSM9455134 Mouse brain, Fc2h, rep1 Mouse brain, Fc2h,
GSM9455135 Mouse brain, Fc2h, rep2 Mouse brain, Fc2h,
GSM9455136 Mouse brain, Fc2h, rep3 Mouse brain, Fc2h,
GSM9455137 Mouse brain, Fc5d, rep1 Mouse brain, Fc5d,
GSM9455138 Mouse brain, Fc5d, rep2 Mouse brain, Fc5d,
GSM9455139 Mouse brain, Fc5d, rep3 Mouse brain, Fc5d,
GSM9455140 Mouse brain, Rc2h, rep1 Mouse brain, Rc2h,
GSM9455141 Mouse brain, Rc2h, rep2 Mouse brain, Rc2h,
GSM9455142 Mouse brain, Rc2h, rep3 Mouse brain, Rc2h,
GSM9455143 Mouse brain, Rc5d, rep1 Mouse brain, Rc5d,
GSM9455144 Mouse brain, Rc5d, rep2 Mouse brain, Rc5d,
GSM9455145 Mouse brain, Rc5d, rep3 Mouse brain, Rc5d,

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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.