Functional dissection of enhancers in 2-Cell embryo with an in vitro model.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 37 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
- 37 samples: 13 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.
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 GSE283389_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 PRJNA1193554 and SRA study SRP548966. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 28 samples.
How we read this: 13 replicated groups read from 37 sample titles; they account for 28 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.
- GSM8660592 GFP negative ATAC rep1 GFP negative ATAC
- GSM8660593 GFP negative ATAC rep2 GFP negative ATAC
- GSM8660594 GFP positive ATAC rep1 GFP positive ATAC
- GSM8660595 GFP positive ATAC rep2 GFP positive ATAC
- GSM8660596 GFP negative input rep1 GFP negative input
- GSM8660597 GFP negative H3K4me1 rep1 GFP negative H3K4me1
- GSM8660598 GFP positive input rep1 GFP positive input
- GSM8660599 GFP positive H3K4me1 rep1 GFP positive H3K4me1
- GSM8660600 GFP negative input rep2 GFP negative input
- GSM8660601 GFP positive input rep2 GFP positive input
- GSM8660602 GFP negative H3K4me1 rep2 GFP negative H3K4me1
- GSM8660603 GFP positive H3K4me1 rep2 GFP positive H3K4me1
- GSM8660604 GFP positive H3K4me3 rep1 GFP positive H3K4me3
- GSM8660605 GFP positive H3K27ac rep1 GFP positive H3K27ac
- GSM8660606 GFP negative H3K4me3 rep1 GFP negative H3K4me3
- GSM8660607 GFP negative H3K4me3 rep2 GFP negative H3K4me3
- GSM8660608 GFP negative H3K27ac rep1 GFP negative H3K27ac
- GSM8660609 GFP negative H3K27ac rep2 GFP negative H3K27ac
- GSM8660610 GFP positive H3K4me3 rep2 GFP positive H3K4me3
- GSM8660611 GFP positive H3K27ac rep2 GFP positive H3K27ac
- GSM8660612 mESC scRNAseq
- GSM8660613 DUX-induced 2CLCs scRNAseq
- GSM8660614 2C like cells STARR input
- GSM8660615 2C like cells STARR rep1 [2C_1_S6_L002]
- GSM8660616 2C like cells STARR rep1 [2C_1_S6_L004]
- GSM8660617 2C like cells STARR rep2
- GSM8660618 Late 2C STARR rep1 Late 2C STARR
- GSM8660619 Late 2C STARR rep2 Late 2C STARR
- GSM8660620 Late 2C STARR input
- GSM8660621 lncRNAseq GFP negative_rep1 lncRNAseq GFP negative
- GSM8660622 lncRNAseq GFP negative_rep2 lncRNAseq GFP negative
- GSM8660623 lncRNAseq GFP negative_rep3 lncRNAseq GFP negative
- GSM8660624 lncRNAseq GFP positive_rep1 lncRNAseq GFP positive
- GSM8660625 lncRNAseq GFP positive_rep2 lncRNAseq GFP positive
- GSM8660626 lncRNAseq GFP positive_rep3 lncRNAseq GFP positive
- GSM9797980 GFP negative p300
- GSM9797981 GFP positive p300
- GSE222656 RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited 40 samples shares 2-cell, embryo
- GSE247083 Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons 38 samples shares 2-cell, embryo
- GSE217970 Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators 164 samples shares enhancers, embryo
- GSE178686 Quantitative comparison of in vitro and in vivo embryogenesis at a single cell resolution 14 samples shares embryo, vitro
- GSE282421 USP17L promotes the 2-cell program through deubiquitination of H2AK119ub1 and ZSCAN4 [ChIP-Seq] 18 samples shares 2-cell
- GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares embryo
- GSE278416 3D Chromatin organization of signal-induced specific enhancers safeguards early ESC differentiation by promoting cluster gene expression 40 samples shares enhancers
- GSE218598 Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo 38 samples shares embryo
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.