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Single cell RNAseq of brian cells in the cortical amygdala with social transmitted food memory

GSE256522 Mus musculus (mouse) Single-cell RNA-seq 3315 samples Submitted 2024/03/09 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 3315 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
3315 samples: 32 conditions, mostly with about 15 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.
Paper
The cortical amygdala consolidates a socially transmitted long-term memoryNature · 2024
Summary (written by the submitters)
Social communication guides decision making that is essential for survival. Social transmission of food preference (STFP) is an ecologically relevant memory paradigm in which an animal learns a desirable food odor from other animals in a social context. How food-preference memory is acquired, consolidated, and stored is unclear. Here, we identify a circuit involving the posteromedial nucleus of the cortical amygdala (COApm) as a computational center that integrates social and sensory olfactory inputs for long-term STFP memory consolidation.
Read the full summary ↓
Blocking synaptic signaling by the COApm circuit selectively abolished STFP memory consolidation without impairing memory acquisition, storage, or recall. STFP memory consolidation by the COApm depends on synaptic inputs from the accessory olfactory bulb and on synaptic outputs to the anterior olfactory nucleus and requires protein synthesis, suggesting a gene expression mechanism. Deep single-cell and spatial transcriptomics revealed robust but distinct gene expression signatures induced by STFP memory formation in the COApm consistent with synapse restructuring. Our data thus define a neural circuit for consolidation of a socially communicated long-term memory, thereby mechanistically distinguishing protein synthesis-dependent memory consolidation from memory acquisition, storage, or retrieval.
Published in
The cortical amygdala consolidates a socially transmitted long-term memory
Liu Z, Sun W, Ng YH et al. · Nature 2024 · PMID 38961294 · doi:10.1038/s41586-024-07632-5
This dataset
Open GSE256522 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 GSE256522_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 PRJNA1079825 and SRA study SRP491468. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38961294) ↗
Study design
32 conditions, mostly with about 15 replicates each
HC_M1P1_D ×20 HC_M1P1_E ×20 HC_M1P1_A ×19 HC_M1P1_F ×18 HC_M1P1_K ×18 HC_M1P1_L ×17 HC_M1P1_M ×17 HC_M1P2_L ×16 +24 more

Supports a between-group comparison across 400 samples.

How we read this: 32 replicated groups read from the first 400 of 3315 sample titles; they account for 400 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

+ 3275 more — browse all 3315 samples with per-sample file links →

Datasets on a similar topic

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