GEO series

Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors

GSE211437 Mus musculus (mouse) Single-nucleus RNA-seq 12 samples Submitted 2024/04/01 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 12 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). 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: 12 samples: 4 × Dorsal striatum vs 3 × Central amygdala vs 3 × Tail of striatum vs 2 × Amygdalostriatal transition areaGroups 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 amygdalostriatal transition zone (ASt) is anatomically poised to provide a shortcut between corticolimbic and basal ganglia circuitry, and mediate behavioral responses to stimuli in parallel with the amygdala. Like the amygdala, the ASt receives converging sensory input from thalamic and cortical pathways. However, the projections of the ASt are distinct from canonical outputs of the amygdala complex, and are integrated with striatal circuits involved in action selection.

Read the full summary ↓

Despite this intriguing circuit connectivity, the function of the ASt is almost completely unknown. In the present study, we collected cellular resolution recordings of genetically-defined neurons during a valence discrimination task to interrogate the functional role of ASt circuitry, and characterized the transcriptomic profile of the ASt in comparison to neighboring regions. We find that ASt neurons, and specifically, ASt neurons expressing dopamine receptor 2 (D2+), robustly encode sustained conditioned responses to cues of negative valence. Selective inhibition of D2+ ASt neurons was found to cause a striking reduction in conditioned fear responses. We also used single-nucleus RNA sequencing to generate a comprehensive profile of gene expression in ASt neurons, and found that the ASt is genetically distinct from adjacent GABAergic brain regions. RNAscope labelling also confirmed there is a greater proportion of D2+ neurons than D1+ neurons in the ASt, a unique feature compared to other regions of the striatum. Together, our findings provide the first evidence the ASt is a critical structure for encoding learned associations to direct motivated behavior.

This dataset

Open GSE211437 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 GSE211437_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 PRJNA870402 and SRA study SRP393114. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

4 × Dorsal striatum vs 3 × Central amygdala vs 3 × Tail of striatum vs 2 × Amygdalostriatal transition area

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 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

GSM6470102 Amygdalostriatal transition area biological replicate 1 Amygdalostriatal transi…
GSM6470103 Amygdalostriatal transition area biological replicate 2 Amygdalostriatal transi…
GSM6470104 Central amygdala biological replicate 1 Central amygdala
GSM6470105 Central amygdala biological replicate 2 Central amygdala
GSM6470106 Central amygdala biological replicate 3 Central amygdala
GSM6470107 Dorsal striatum biological replicate 1 Dorsal striatum
GSM6470108 Dorsal striatum biological replicate 2 Dorsal striatum
GSM6470109 Dorsal striatum biological replicate 3 Dorsal striatum
GSM6470110 Dorsal striatum biological replicate 4 Dorsal striatum
GSM6470111 Tail of striatum biological replicate 1 Tail of striatum
GSM6470112 Tail of striatum biological replicate 2 Tail of striatum
GSM6470113 Tail of striatum biological replicate 3 Tail of striatum

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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.