Single nuclei RNA and ATAC sequencing of mouse trigeminal ganglia at baseline and in atopic dermatitis-like disease.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 14 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
- 14 samples: 14 samples, each with a distinct title — no replicated groupsGroups 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE190309_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA786622 and SRA study SRP349463. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 14 sample titles: 14 distinct titles with little repetition. 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.
- GSM5719612 TG_EtOH_bulk_12d_GEX
- GSM5719613 TG_MC903_bulk_12d_GEX
- GSM5719614 TG_EtOH_neur_enr_12d_GEX
- GSM5719615 TG_MC903_neur_enr_3d_GEX
- GSM5719616 TG_MC903_neur_enr_12d_GEX
- GSM5719617 TG_EtOH_neur_enr_12d_plus30d_GEX
- GSM5719618 TG_MC903_neur_enr_12d_plus30d_GEX
- GSM5719619 TG_EtOH_bulk_12d_ATAC
- GSM5719620 TG_MC903_bulk_12d_ATAC
- GSM5719621 TG_EtOH_neur_enr_12d_ATAC
- GSM5719622 TG_MC903_neur_enr_3d_ATAC
- GSM5719623 TG_MC903_neur_enr_12d_ATAC
- GSM5719624 TG_EtOH_neur_enr_12d_plus30d_ATAC
- GSM5719625 TG_MC903_neur_enr_12d_plus30d_ATAC
- GSE316925 Transcriptome changes in trigeminal ganglia in the mouse chronic constriction injury of the infraorbital nerve model - role of TRPM3. 136 samples shares trigeminal, ganglia
- GSE312302 NMuMG PBRM1 RNA-seq, ATAC-seq, and ChIP-seq 171 samples shares atac
- GSE321762 Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk [scRNA-seq and scATAC-seq] 54 samples shares atac
- GSE292377 Step-wise signal integration governs adaptive programming of lymphocytes [bulkRNA-seq and ATAC-seq] 41 samples shares atac
- GSE334540 Single nucleus multiome (RNAseq and ATACseq) of male and female mouse pituitary 32 samples shares atac
- GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares atac
- GSE327645 BACH1 acts as a pioneer repressor to enable macrophage plasticity and adaptation across tissues and inflammatory contexts [RNA-seq/ATAC-seq] 28 samples shares atac
- GSE325227 CD69 regulates the tissue dynamics of epigenetically imprinted memory CD4+ T cells [RNA-seq_ATAC-seq] 22 samples shares atac
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.