RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 21 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
- 21 samples: 10 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
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 GSE236161_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 PRJNA989148 and SRA study SRP446623. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 10 replicated groups read from 21 sample titles; they account for 21 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.
- GSM7518892 2C_rep1 2C
- GSM7518893 2C_rep2 2C
- GSM7518894 8C_rep1 8C
- GSM7518895 8C_rep2 8C
- GSM7518896 CX22_rep1 CX22
- GSM7518897 CX22_rep2 CX22
- GSM7518898 CX45_rep1 CX45
- GSM7518899 CX45_rep2 CX45
- 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
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares transcription, chromatin
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares transcription, chromatin
- GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares transcription, chromatin
- GSE274040 Transcriptional and chromatin accessibility landscapes of hematopoiesis in a mouse model of breast cancer 16 samples shares transcription, chromatin
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares architecture, chromatin
- GSE283906 RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling 10 samples shares transcription, chromatin
- GSE73952 Distinct features in establishing H3K4me3 and H3K27me3 in pre-implantation embryos 67 samples shares establishing, embryos
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.