Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain [Mouse snATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 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.
- Paper
- Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predispositionCell reports · 2024
Read the full summary ↓
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 GSE253952_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 PRJNA1067989 and SRA study SRP485381. 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 12 sample titles: 12 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.
- GSM8030979 Replicate 1, mouse mixed pool, snATAC
- GSM8030980 Replicate 2, mouse mixed pool, snATAC
- GSM8030981 Replicate 3, mouse mixed pool, snATAC
- GSM8030982 Replicate 4, mouse mixed pool, snATAC
- GSM8030983 Replicate 5, mouse mixed pool, snATAC
- GSM8030984 Replicate 6, mouse mixed pool, snATAC
- GSM8030985 Replicate 7, mouse mixed pool, snATAC
- GSM8030986 Replicate 8, mouse mixed pool, snATAC
- GSM8030987 Replicate 9, mouse mixed pool, snATAC
- GSM8030988 Replicate 10, mouse mixed pool, snATAC
- GSM8030989 Replicate 11, mouse mixed pool, snATAC
- GSM8030990 Replicate 12, mouse mixed pool, snATAC
- GSE253951 Conserved dorsal horn neuron subtype-specific enhancers are implicated in the genetic risk of chronic pain [Mouse Xenium] 2 samples shares subtype-specific, implicated, conserved, enhancers, genetic, chronic, dorsal
- GSE255016 A chronic, low-dose treatment with methamphetamine modulates genes implicated in neurodegeneration in a transgenic model of NeuroHIV 24 samples shares implicated, chronic
- GSE242069 Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation 6 samples shares conserved, genetic
- GSE254693 A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex 70 samples shares conserved
- GSE256297 Conserved helical motifs in the Ikaros IDR mediate NuRD corepressor interaction and transcriptional repression [ChIP-seq] 32 samples shares conserved
- GSE254692 A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT&RUN 22] 28 samples shares conserved
- GSE254691 A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex [CUT&RUN] 24 samples shares conserved
- GSE292043 A conserved differentiation program facilitates inhibitory neuron production in the developing mouse and human cerebellum 24 samples shares conserved
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.