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Knockdown and knockout of the Integrated Stress Response (ISR) and ATF4 in cultures of adult mouse dorsal root ganglia

GSE336472 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2026/07/21 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 7 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)
The Activating Transcription Factor-4 (ATF4) contributes to pro-regenerative transcriptional responses following optic axon damage. Here we use an in vitro model of axon regeneration to investigate the contributions of ATF4 to the transcriptional injury response of adult mouse sensory neurons of the dorsal root ganglion (DRG). We find that, in contrast to optic axon injury, the upregulation of the pro-regenerative transcription factor ATF3 is not ATF4-dependent, and without that contribution, ATF4 instead limits adult DRG axon regrowth in collaboration with C/EBPgamma.
Read the full summary ↓
Knockout or knockdown of ATF4 enhances axon regeneration in this model while regulating a collection of genes strongly overlapping with those regulated by C/EBPgamma. We find that overexpression of ATF4 suppresses axon regeneration in a C/EBPgamma-dependent manner. This effect, however, is not a simple reciprocal of ATF4 knockout, as it is also correlated with suppression of ATF3- and c-Jun-dependent transcription. Together these findings suggest that axon injury induces an ATF4-dependent transcriptional program that limits regeneration in parallel with pro-regenerative responses.
This dataset
Open GSE336472 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 GSE336472_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 PRJNA1481683 and SRA study SRP712315. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly with about 4 replicates each
DRG culture, wildtype, siCONTROL, t=42h, ×4 DRG culture, wildtype, siAtf4, t=42h, ×4 DRG culture, wildtype, siCebpg, t=42h, ×4 DRG culture, wildtype, siPerk, t=42h, ×4 DRG culture, Atf4.cKO, siCONTROL, t=42h, ×4 DRG culture, Atf4.cKO, siCebpg, t=42h, ×4 DRG culture, ISR.cKO, siCONTROL, t=42h, ×4

Supports a between-group comparison across 28 samples.

How we read this: 7 replicated groups read from 28 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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