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Total and dendritic RNA-sequencing from primary mouse cortical neurons

GSE213012 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2024/03/14 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 32 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
32 samples: 8 conditions, mostly with about 4 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
Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF bindingNature neuroscience · 2024
Summary (written by the submitters)
Activity-dependent protein synthesis is critical for determining changes in dendritic proteomes underlying brain function, yet the mechanisms governing these changes are lacking. Here, we combined proximity-based labeling of dendritic transcriptome, translatome, and proteome to study the dynamics of RNA regulation in activated synapses.
Read the full summary ↓
We discovered that depolarization leads to a switch from RNAs translated under basal conditions to new translation of previously unrecognized subsets of depolarization-dependent transcripts. Dynamically regulated RNAs bound by specific regulatory proteins, including NOVA1, FMRP, and ELAVLs, rapidly generate proteins with roles in mitochondrial regulation, RNA metabolism, translational control, and synaptic signaling in dendrites. Knockdowns of activity-induced dendritic RNAs altered neuronal physiology, underscoring how dynamic switches in the regulation of RNAs encoding coordinated sets of proteins underlie synaptic plasticity.
Published in
Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding
Hacisuleyman E, Hale CR, Noble N et al. · Nature neuroscience 2024 · PMID 38589584 · doi:10.1038/s41593-024-01615-5
This dataset
Open GSE213012 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 GSE213012_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 PRJNA878777 and SRA study SRP396433. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38589584) ↗
Study design
8 conditions, mostly with about 4 replicates each
REST_PSD95_in ×4 REST_PSD95_pd ×4 DEP_PSD95_in ×4 DEP_PSD95_pd ×4 REST_PAN_in ×3 REST_PAN_pd ×3 DEP_PAN_in ×3 DEP_PAN_pd ×3 +4 more

Supports a between-group comparison across 28 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 28 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
Datasets on a similar topic

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