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Endogenous patterned activity-regulated genes specifically regulate different phases of synaptogenesis in the auditory system

GSE283753 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2024/12/12 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 21 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
21 samples: 6 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.
Summary (written by the submitters)
In the auditory system, spatiotemporal patterning of correlated activity that originates in immature hair cells (HC) instructs refinement of synaptic connections and tonotopy. Patterned activity-dependent synaptic pruning requires the interplay between Hebbian plasticity and activity-regulated genes (ARGs). However, the genetic basis of this process is incompletely understood.
Read the full summary ↓
Here we demonstrate that developing spiral ganglion neurons (SGNs) transiently generate discrete bursts of spikes and that blocking burst activity in this critical window causes profound deafness in mice. Using RNA sequencing, we profile ARG programs by genetically disrupting endogenous activity patterns of SGNs without changing spontaneous firing of inner HCs. Gene knockdown reveals that Nptx2 mediates initial synaptic formations at early stage, whereas Them5, which is important for cardiolipin remodeling that enhances mitochondrial function, specifically regulates synaptic pruning at later stage of development. These results suggest that ARGs dictate different phases of synaptogenesis and that Them5-depedent mitochondrial function might underlie synaptic pruning.
This dataset
Open GSE283753 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 GSE283753_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 PRJNA1195347 and SRA study SRP549988. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 4 replicates each
control_apex ×4 control_base ×4 DN-mHCN2_apex ×4 DN-mHCN2_base ×3 truncated_SK3_apex ×3 truncated_SK3_base ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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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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.