The landscape of accessible chromatin in mammalian pre-implantation embryos (RNA-Seq)
Single-cell RNA-seq · mouse · 32 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 32 samples
- 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.
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 GSE66582_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA277361 and SRA study SRP055882. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 32 more — browse all 32 samples with per-sample file links →
- GSE296438 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [scRNA-seq & scATAC-seq] 10 samples shares accessible, chromatin, rna-seq
- GSE166225 Inference of emergent spatio-temporal processes from single-cell sequencing reveals feedback between de novo DNA methylation and chromatin condensates [RNA-seq] 288 samples shares chromatin, rna-seq
- GSE276155 RBBP5 is an epigenetic regulator of mammalian hepatic 12h oscillator [RNA-seq] 96 samples shares mammalian, rna-seq
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares chromatin, rna-seq
- GSE73952 Distinct features in establishing H3K4me3 and H3K27me3 in pre-implantation embryos 67 samples shares pre-implantation, embryos
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares chromatin, embryos
- GSE315771 HDI-STARR-seq library profiling of differential accessible chromatin regions (DARs) in livers of male, female and male treated with continuous growth hormone (cGH) mice. 12 samples shares accessible, chromatin
- GSE307620 Spatial chromatin architecture and accessibility co-profiling of mammalian tissues 2 samples shares chromatin, mammalian
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.