← BioTransfer GEO Dataset Finder
GEO series

Persistent large-scale changes in alternative splicing in prefrontal cortical neuron types following psychedelic exposure

GSE286904 Mus musculus (mouse) RNA-seq (gene expression) 118 samples Submitted 2025/01/16 Platform GPL34328Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 118 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
118 samples: 108 distinct titles, 10 of them repeatedGroups 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 goal of this project was to assess the cell-type specific transcriptomic changes induced by psychedelics in a rodent model. We used the RiboTag technique to isolate RNA from genetically-defined neuronal subtypes in the mouse prefrontal cortex. Conditional tagging of the ribosomal protein Rpl22 was done with Pvalb-Cre, Cux2-CreERT, and Rbp4-Cre for PV interneurons, L2/3 pyramidal neurons, and L5 pyramidal neurons respectively.
Read the full summary ↓
We deep-sequenced (~100 million paired-end reads) the RNAs using Illumina platforms. We found cell-type specific gene expression and alternative splicing changes associated with psychedelics, providing a essential resource for understanding the various effects of psychedelics on cortical cell types and functions.
This dataset
Open GSE286904 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 GSE286904_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 PRJNA1210517 and SRA study SRP557339. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
108 distinct titles, 10 of them repeated
Rbp4,F,Saline,48hrs,rep1,b ×2 Rbp4,M,Saline,48hrs,rep2,b ×2 Cux2ERT,M,Saline,48hrs,rep2,b ×2 Rbp4,F,Saline,48hrs,rep3,b ×2 Rbp4,F,Saline,48hrs,rep4,b ×2 Rbp4,M,Saline,48hrs,rep5,b ×2 Cux2ERT,M,Saline,48hrs,rep3,b ×2 Cux2ERT,M,Saline,48hrs,rep4,b ×2 +2 more

How we read this: Read from 118 sample titles: 108 distinct titles with little repetition. 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

+ 78 more — browse all 118 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.