Establishment of chromatin architecture interplays with embryo hypertranscription
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 158 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
- 158 samples: 51 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
- Establishment of chromatin architecture interplays with embryo hypertranscriptionNature · 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 GSE200323_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 PRJNA824060 and SRA study SRP367893. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 106 samples.
How we read this: 51 replicated groups read from 158 sample titles; they account for 106 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.
- GSM6031216 CTCF, PN3, rep1 CTCF, PN3,
- GSM6031217 CTCF, PN3, rep2 CTCF, PN3,
- GSM6031218 CTCF, Early2C, rep1 CTCF, Early2C,
- GSM6031219 CTCF, Early2C, rep2 CTCF, Early2C,
- GSM6031220 CTCF, Late2C, rep1 CTCF, Late2C,
- GSM6031221 CTCF, Late2C, rep2 CTCF, Late2C,
- GSM6031222 CTCF, 8C, rep1 CTCF, 8C,
- GSM6031223 CTCF, 8C, rep2 CTCF, 8C,
- GSM6031224 CTCF, ICM, rep1 CTCF, ICM,
- GSM6031225 CTCF, ICM, rep2 CTCF, ICM,
- GSM6031226 CTCF, EPI, rep1 CTCF, EPI,
- GSM6031227 CTCF, EPI, rep2 CTCF, EPI,
- GSM6031228 CTCF, mESC, rep1 CTCF, mESC,
- GSM6031229 CTCF, mESC, rep2 CTCF, mESC,
- GSM6031230 SMC3, PN3, rep1 SMC3, PN3,
- GSM6031231 SMC3, PN3, rep2 SMC3, PN3,
- GSM6031232 SMC3, Early2C, rep1 SMC3, Early2C,
- GSM6031233 SMC3, Early2C, rep2 SMC3, Early2C,
- GSM6031236 SMC3, 8C, rep1 SMC3, 8C,
- GSM6031237 SMC3, 8C, rep2 SMC3, 8C,
- GSM6031240 SMC3, EPI, rep1 SMC3, EPI,
- GSM6031241 SMC3, EPI, rep2 SMC3, EPI,
- GSM6031242 SMC3, mESC
- GSM6215368 RNA_8C_heatshock_rep1 RNA_8C_heatshock
- GSM6215369 RNA_8C_heatshock_rep2 RNA_8C_heatshock
- GSM6215370 RNA_8C_heatshock_control
- GSM6215371 SMC3_8C_heatshock
- GSM6215372 SMC3_8C_heatshock_control
- GSM6215373 SMC3_DMSO_control_for_DRB
- GSM6215374 SMC3_DRB_2h
- GSM6215375 SMC3_DRB_4h
- GSM6288599 CTCF Late2C_ADNP_OE_rep1 CTCF Late2C_ADNP_OE
- GSM6288600 CTCF Late2C_ADNP_OE_rep2 CTCF Late2C_ADNP_OE
- GSM6288601 CTCF Late2C_GFP_control_for_ADNP_OE
- GSM9185289 MicroC_8C
- GSM9185290 HiC_Blastocyst_ADNPKO_control
- GSM9185291 HiC_Blastocyst_ADNPKO_rep1 HiC_Blastocyst_ADNPKO
- GSM9185292 HiC_Blastocyst_ADNPKO_rep2 HiC_Blastocyst_ADNPKO
- GSM9185293 HiC_8C_DMSO_control_for_4hDRB
- GSM9185294 HiC_8C_DRB_4h_rep1 HiC_8C_DRB_4h
+ 118 more — browse all 158 samples with per-sample file links →
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares establishment, chromatin, embryo
- GSE206159 Stepwise de novo establishment of inactive X chromosome architecture in early development [Embryo RNA-seq] 42 samples shares establishment, architecture, embryo
- GSE236161 RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos 21 samples shares architecture, chromatin, embryo
- GSE236160 RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos [ChIP-seq] 13 samples shares architecture, chromatin, embryo
- GSE263441 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [RNA-Seq] 10 samples shares establishment, chromatin, embryo
- 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
- GSE206011 Stepwise de novo establishment of inactive X chromosome architecture in early development 262 samples shares establishment, architecture
- GSE262551 A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation 255 samples shares architecture, chromatin
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.