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Compartmentalisation of m6A (N6-methyladenosine) methylated RNA in somatic or axonal subcellular locations is dependent on Nerve Growth Factor (NGF) state in sympathetic neurons [Axon-meRIP-seq]

GSE336756 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2026/07/01 Platform GPL30172
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: 4 × Control_CB vs 4 × Control_Ax vs 4 × Restim_CB vs 4 × Restim_AxGroups 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)
Sympathetic neurons were culture in compartmentalised chambers in medium with NGF (control condition). Cells were then subjected to NGF starvation for 18 hours followed by 1 hour of restimulation. RNA was collected from either cell bodies (CB) or axons (Ax) from these neurons for meRIP-seq. Here, we find a strong compartmentalisation effect, in which RNA is hypermethylated in axons in both control and restimulated conditions.
Read the full summary ↓
We also find that a select few RNA species are hypermethylated in restimulated axons compared to control axons, suggesting a fast time-dependent function for m6A marks in these RNAs.
This dataset
Open GSE336756 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 GSE336756_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 PRJNA1482515 and SRA study SRP712948. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × Control_CB vs 4 × Control_Ax vs 4 × Restim_CB vs 4 × Restim_Ax

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 32 sample titles; they account for 16 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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