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Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

GSE230720 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2025/05/16 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 4 × PC 24h Inj vs 4 × PC 24h Na vs 4 × PC 72h Inj vs 4 × PC 72h NaGroups 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
Repeat-element RNAs integrate a neuronal growth circuitCell · 2025
Summary (written by the submitters)
To map the loci of B2-SINE expressed in DRG which are regulated by sciatic nerve injury, paired-end RNAseq was carried on DRG neurons following sciatic nerve injury at 24h and 72h (3d) after injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.
Published in
Repeat-element RNAs integrate a neuronal growth circuit
Zahavi EE, Koppel I, Kawaguchi R et al. · Cell 2025 · PMID 40381624 · doi:10.1016/j.cell.2025.04.030
This dataset
Open GSE230720 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 GSE230720_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 PRJNA962457 and SRA study SRP434816. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40381624) ↗
Study design
4 × PC 24h Inj vs 4 × PC 24h Na vs 4 × PC 72h Inj vs 4 × PC 72h Na

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 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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