RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
- 13 samples: 6 conditions, mostly in duplicateGroups 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
- RNA polymerase I is essential for driving the formation of 3D genome in early embryonic development in mouse, but not in humanGenome medicine · 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 GSE236160_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 PRJNA989158 and SRA study SRP446623. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 13 samples.
How we read this: 6 replicated groups read from 13 sample titles; they account for 13 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.
- GSM7519042 POLR1A_1cell_rep1 POLR1A_1cell
- GSM7519043 POLR1A_1cell_rep2 POLR1A_1cell
- GSM7519044 POLR1A_2cell_cx5461_rep1 POLR1A_2cell_cx5461
- GSM7519045 POLR1A_2cell_cx5461_rep2 POLR1A_2cell_cx5461
- GSM7519046 POLR1A_2cell_early_rep1 POLR1A_2cell_early
- GSM7519047 POLR1A_2cell_early_rep2 POLR1A_2cell_early
- GSM7519048 POLR1A_2cell_early_rep3 POLR1A_2cell_early
- GSM7519049 POLR1A_2cell_late_rep1 POLR1A_2cell_late
- GSM7519050 POLR1A_2cell_late_rep2 POLR1A_2cell_late
- GSM7519051 POLR1A_8cell_rep1 POLR1A_8cell
- GSM7519052 POLR1A_8cell_rep2 POLR1A_8cell
- GSM7519053 lgG_2cell_rep1 lgG_2cell
- GSM7519054 lgG_2cell_rep2 lgG_2cell
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares transcription, architecture, chromatin
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples shares architecture, chip-seq
- GSE73952 Distinct features in establishing H3K4me3 and H3K27me3 in pre-implantation embryos 67 samples shares establishing, embryos
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, chromatin
- GSE326173 Nuclear receptor Nur77 resolves the inflammatory response of macrophages primarily by regulating expression of AP-1 transcription factors and their target genes [ChIP-seq] 42 samples shares transcription, chip-seq
- GSE324933 DGCR8 promotes RNA polymerase II pause release independently of DROSHA [ChIP-seq] 32 samples shares polymerase, chip-seq
- GSE324864 HP1B and H3K9me3 Regulate Olfactory Receptor Choice and 2 Transcriptional Identity [ChIP-seq] 28 samples shares transcription, chip-seq
- GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares transcription, chip-seq
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.