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Shared and divergent transcriptomic regulation in nucleus accumbens D1 and D2 medium spiny neurons by cocaine

GSE272823 Mus musculus (mouse) RNA-seq (gene expression) 75 samples Submitted 2024/10/09 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 75 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
75 samples: 8 conditions, mostly with about 10 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
Cell type-specific epigenetic priming of gene expression in nucleus accumbens by cocaineScience advances · 2024
Summary (written by the submitters)
Substance use disorders (SUDs) induce widespread molecular dysregulation in nucleus accumbens (NAc), a brain region pivotal for coordinating motivation and reward, which is linked to neural and behavioral disturbances promoting addiction. Despite the overlapping symptomatology of SUDs, different drug classes exert partly unique influences on neural circuits, cell types, physiology, and gene expression.
Read the full summary ↓
To better understand common and divergent molecular mechanisms governing SUD pathology, we characterized the cell-type-specific restructuring of the NAc transcriptional landscape after psychostimulant or opioid exposure. We combined fluorescence-activated nuclei sorting and RNA sequencing to profile NAc D1 and D2 medium spiny neurons (MSNs) across cocaine exposure paradigms, including initial exposure, prolonged withdrawal after repeated exposure, and re-exposure post-withdrawal. Our analyses reveal that D1 MSNs display many convergent transcriptional responses across the two drugs, whereas D2 MSNs manifest highly divergent responses, with morphine causing far more adaptations in this cell type.
Published in
Cell type-specific epigenetic priming of gene expression in nucleus accumbens by cocaine
Mews P, Van der Zee Y, Gurung A et al. · Science advances 2024 · PMID 39365860 · doi:10.1126/sciadv.ado3514
This dataset
Open GSE272823 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 GSE272823_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 PRJNA1138820 and SRA study SRP521465. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39365860) ↗
Study design
8 conditions, mostly with about 10 replicates each
Coc_D1_CC ×10 Coc_D1_SS ×10 Coc_D2_CC ×10 Coc_D2_CS ×10 Coc_D1_SC ×9 Coc_D2_SC ×9 Coc_D2_SS ×9 Coc_D1_CS ×8

Supports a between-group comparison across 75 samples.

How we read this: 8 replicated groups read from 75 sample titles; they account for 75 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

+ 35 more — browse all 75 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.