Deciphering transcriptional activities in mouse early embryo
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 26 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
- 26 samples: 9 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
- Deciphering transcription activity of mammalian early embryos unveils on/off of zygotic genome activation by protein translation/degradationCell reports · 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 GSE241197_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 PRJNA1006284 and SRA study SRP455725. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 26 sample titles; they account for 18 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.
- GSM7719180 2C_IVF_IgG_1
- GSM7719181 2C_IVF_PolII_Ps_1 2C_IVF_PolII_Ps
- GSM7719182 2C_IVF_PolII_Ps_2 2C_IVF_PolII_Ps
- GSM7719183 4C_IVF_IgG_1
- GSM7719184 4C_IVF_PolII_Ps_1 4C_IVF_PolII_Ps
- GSM7719185 4C_IVF_PolII_Ps_2 4C_IVF_PolII_Ps
- GSM7719186 8cell_IgG
- GSM7719187 8cell_Ps_1 8cell_Ps
- GSM7719188 8cell_Ps_2 8cell_Ps
- GSM7719189 FGO_IgG
- GSM7719190 FGO_PolII_Ps_1 FGO_PolII_Ps
- GSM7719191 FGO_PolII_Ps_2 FGO_PolII_Ps
- GSM7719192 IVF_6h_IgG
- GSM7719193 IVF_6h_PolII_Ps_1 IVF_6h_PolII_Ps
- GSM7719194 IVF_6h_PolII_Ps_2 IVF_6h_PolII_Ps
- GSM7719195 L1C_IVF_IgG_1
- GSM7719196 L1C_IVF_PolII_Ps_1 L1C_IVF_PolII_Ps
- GSM7719197 L1C_IVF_PolII_Ps_2 L1C_IVF_PolII_Ps
- GSM7719198 L2C_IVF_IgG_1
- GSM7719199 L2C_IVF_PolII_Ps_1 L2C_IVF_PolII_Ps
- GSM7719200 L2C_IVF_PolII_Ps_2 L2C_IVF_PolII_Ps
- GSM7719201 Mla_IVF_IgG_1
- GSM7719202 Mla_IVF_PolII_Ps_1 Mla_IVF_PolII_Ps
- GSM7719203 Mla_IVF_PolII_Ps_2 Mla_IVF_PolII_Ps
- GSM7719204 P14_Oo_PolII_Ps_1 P14_Oo_PolII_Ps
- GSM7719205 P14_Oo_PolII_Ps_2 P14_Oo_PolII_Ps
- GSE264614 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq] 44 samples shares embryo, early
- GSE296991 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [CATCH-seq of early embryo] 23 samples shares embryo, early
- GSE217970 Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators 164 samples shares embryo, early
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares embryo, early
- GSE229238 DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2] 42 samples shares embryo, early
- GSE296992 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [RNA-seq of early embryo] 26 samples shares embryo, early
- GSE252418 Subchronic elevation in ambient temperature drives alterations to the sperm epigenome and accelerates early embryonic development in mice 83 samples shares embryo, early
- GSE295196 m6A RNA methylation in the maintenance of X-chromosome inactivation and X to autosome dosage compensation in early embryogenesis [RNA-Seq] 14 samples shares embryo, early
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.