Mapping of Chromatin Architecture and Enhancer-Promoter Interactions in the Cochlea
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 16 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
- 16 samples: 5 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.
- Paper
- Mapping of chromatin architecture and enhancer-promoter interactions in the cochleaFrontiers in molecular biosciences · 2025
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 GSE305205_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 PRJNA1304594 and SRA study SRP608211. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 5 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.
- GSM9164803 P0 Cochlea replicate 1 P0 Cochlea
- GSM9164804 P0 Cochlea replicate 2 P0 Cochlea
- GSM9164805 P0 Cochlea replicate 3 P0 Cochlea
- GSM9164806 P0 Cochlea replicate 4 P0 Cochlea
- GSM9164807 P0 Cochlea umiATAC replicate 1 P0 Cochlea umiATAC
- GSM9164808 P0 Cochlea umiATAC replicate 2 P0 Cochlea umiATAC
- GSM9164809 P0 Cochlea CutRun H3K4me1 replicate 1 P0 Cochlea CutRun H3K4m…
- GSM9164810 P0 Cochlea CutRun H3K4me1 replicate 2 P0 Cochlea CutRun H3K4m…
- GSM9164811 P0 Cochlea CutRun H3K4me1 replicate 3 P0 Cochlea CutRun H3K4m…
- GSM9164812 P0 Cochlea CutRun H3K27ac replicate 1 P0 Cochlea CutRun H3K27…
- GSM9164813 P0 Cochlea CutRun H3K27ac replicate 2 P0 Cochlea CutRun H3K27…
- GSM9164814 P0 Cochlea CutRun H3K27ac replicate 3 P0 Cochlea CutRun H3K27…
- GSM9164815 P0 Cochlea CutRun CTCF replicate 1 P0 Cochlea CutRun CTCF
- GSM9164816 P0 Cochlea CutRun CTCF replicate 2 P0 Cochlea CutRun CTCF
- GSM9164817 P0 Cochlea CutRun CTCF replicate 3 P0 Cochlea CutRun CTCF
- GSM9164818 P0 Cochlea CutRun CTCF replicate 4 P0 Cochlea CutRun CTCF
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares architecture, chromatin
- GSE314917 FACT maintains nucleosomes around promoters and opposes to the spreading of chromatin factors, thereby playing a major role in chromatin architecture 115 samples shares architecture, chromatin
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares architecture, chromatin
- GSE310322 Mapping self-associating chromatin hubs identifies Id proteins as key determinants of exhausted T cell fate 37 samples shares chromatin, mapping
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares chromatin, mapping
- GSE249077 Mapping the female mouse chromatin accessibility landscape by UUATAC-seq 23 samples shares chromatin, mapping
- GSE249834 Impact of Chromatin Immunoprecipitation Crosslinking Conditions on Selective Genomic Interactions by NF‐κB Family Members 21 samples shares interactions, chromatin
- GSE263333 Spatial-Mux-seq: Multiplexed spatial mapping of chromatin features, transcriptome, and proteins at tissue scale 12 samples shares chromatin, mapping
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.