← BioTransfer GEO Dataset Finder
GEO series

Three-dimensional chromatin architecture in DRG neurons following sciatic nerve injury in WT and Rad21 KO mice.

GSE249687 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 52 samples Submitted 2024/08/29 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 52 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
52 samples: 18 conditions, mostly in triplicateGroups 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
Three-dimensional chromatin mapping of sensory neurons reveals that promoter-enhancer looping is required for axonal regenerationProceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
Axonal regeneration after injury requires active gene transcription. Whether chromatin 3D genome architecture is required for the neuronal regenerative transcriptional programme is unexplored. Here we addressed this question in a model of sciatic nerve injury by combinatorial Hi-C, promoter-capture Hi-C, CUT&Tag for H3K27ac and RNA-seq in wild-type and cohesin-deficient sensory dorsal root ganglia neurons.
Published in
Three-dimensional chromatin mapping of sensory neurons reveals that promoter-enhancer looping is required for axonal regeneration
Palmisano I, Liu T, Gao W et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 39254997 · doi:10.1073/pnas.2402518121
This dataset
Open GSE249687 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 GSE249687_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1043092 and SRA study SRP473052. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39254997) ↗
Study design
18 conditions, mostly in triplicate
HIC_Sham_WT ×3 HIC_Sciatic nerve crush_WT ×3 HIC_Sham_KO ×3 HIC_Sciatic nerve crush_KO ×3 PromoterHIC_Sham_WT ×3 PromoterHIC_Sciatic nerve crush_WT ×3 PromoterHIC_Sham_KO ×3 PromoterHIC_Sciatic nerve crush_KO ×3 +10 more

Supports a between-group comparison across 52 samples.

How we read this: 18 replicated groups read from 52 sample titles; they account for 52 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

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.