A single-cell atlas of chromatin accessibility in mouse organogenesis
Single-cell RNA-seq · mouse · 68 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 68 samples: 65 distinct titles, 1 of them repeatedGroups 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
- A single-cell atlas of chromatin accessibility in mouse organogenesisNature cell biology · 2024
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 GSE216371_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 PRJNA893359 and SRA study SRP404100. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 68 sample titles: 65 distinct titles with little repetition. 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.
- GSM6671097 SPATAC-seq with mouse organogenesis well-E11A
- GSM6671098 SPATAC-seq with mouse organogenesis well-E11B
- GSM6671099 SPATAC-seq with mouse organogenesis well-E11C
- GSM6671100 SPATAC-seq with mouse organogenesis well-E11D
- GSM6671101 SPATAC-seq with mouse organogenesis well-E11E
- GSM6671102 SPATAC-seq with mouse organogenesis well-E11F
- GSM6671103 SPATAC-seq with mouse organogenesis well-E11G
- GSM6671104 SPATAC-seq with mouse organogenesis well-E11H
- GSM6671105 SPATAC-seq with mouse organogenesis well-E153
- GSM6671106 SPATAC-seq with mouse organogenesis well-E154
- GSM6671107 SPATAC-seq with mouse organogenesis well-E155
- GSM6671108 SPATAC-seq with mouse organogenesis well-E156
- GSM6671109 SPATAC-seq with mouse organogenesis well-E17A
- GSM6671110 SPATAC-seq with mouse organogenesis well-E17B
- GSM6671111 SPATAC-seq with mouse organogenesis well-E17C
- GSM6671112 SPATAC-seq with mouse organogenesis well-E17D
- GSM6671113 SPATAC-seq with mouse organogenesis well-E17E
- GSM6671114 SPATAC-seq with mouse organogenesis well-E17F
- GSM6671115 SPATAC-seq with mouse organogenesis well-E17G
- GSM6671116 SPATAC-seq with mouse organogenesis well-E17H
- GSM6671117 SPATAC-seq with mouse organogenesis well-E18A
- GSM6671118 SPATAC-seq with mouse organogenesis well-E18B
- GSM6671119 SPATAC-seq with mouse organogenesis well-E18C
- GSM6671120 SPATAC-seq with mouse organogenesis well-E18D
- GSM6671121 SPATAC-seq with mouse organogenesis well-E18E
- GSM6671122 SPATAC-seq with mouse organogenesis well-E18F
- GSM6671123 SPATAC-seq with mouse organogenesis well-E18G
- GSM6671124 SPATAC-seq with mouse organogenesis well-E18H
- GSM6671125 SPATAC-seq with mouse organogenesis well-E19A
- GSM6671126 SPATAC-seq with mouse organogenesis well-E19B
- GSM6671127 SPATAC-seq with mouse organogenesis well-E19C
- GSM6671128 SPATAC-seq with mouse organogenesis well-E19D
- GSM6671129 SPATAC-seq with mouse organogenesis well-E19E
- GSM6671130 SPATAC-seq with mouse organogenesis well-E19F
- GSM6671131 SPATAC-seq with mouse organogenesis well-E19G
- GSM6671132 SPATAC-seq with mouse organogenesis well-E19H
- GSM6671133 SPATAC-seq with mouse organogenesis well-E1A
- GSM6671134 SPATAC-seq with mouse organogenesis well-E1B
- GSM6671135 SPATAC-seq with mouse organogenesis well-E1C
- GSM6671136 SPATAC-seq with mouse organogenesis well-E1D
+ 28 more — browse all 68 samples with per-sample file links →
- GSE264229 Mapping the male mouse chromatin accessibility landscape by UUATAC-seq 33 samples shares accessibility, 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 single-cell, chromatin
- GSE246986 Ki67-mediated chromatin accessibility impedes B-cell antigen-receptor gene rearrangement 24 samples shares accessibility, chromatin
- GSE342565 Chromatin accessibility profiling of high endothelial cells (HECs) from mouse peripheral lymph node and Peyer's patch by ATAC-seq 2 samples shares accessibility, chromatin
- GSE294772 Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome] 142 samples shares single-cell, chromatin
- GSE274040 Transcriptional and chromatin accessibility landscapes of hematopoiesis in a mouse model of breast cancer 16 samples shares accessibility, chromatin
- GSE290224 Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle 96 samples shares accessibility, chromatin
- GSE230765 Best practices for differential accessibility analysis in single-cell epigenomics 16 samples shares accessibility, single-cell
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.