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Series GSE121690 Query DataSets for GSE121690
Status Public on Sep 30, 2019
Title Single-cell methylation and accessibility of mouse embryos E4.5 to E7.5. First batch.
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.

We strongly encourage anyone wanting to use these data to first try the parsed data in the link below together with the scripts we used in the paper which can be found in the GitHub repository.

Useful links:
Parsed data: (
Github repository: (
Overall design 758 single cells isolated from mouse embryos at E4.5, E5.5, E6.5 and E7.5 and processed using scNMT-seq (Clark et al 2018)
Contributor(s) Argelaguet R, Mohammed H, Clark SJ, Stapel LC, Krueger C, Kapourani C, Xiang Y, Hanna C, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Krueger F, Xie W, Rugg-Gunn P, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W
Citation(s) 31827285, 33879195
Submission date Oct 23, 2018
Last update date Jul 06, 2022
Contact name Felix Krueger
Organization name Altos Labs
Department Bioinformatics
Street address Granta Park
City Cambridge
ZIP/Postal code CB21 6GP
Country United Kingdom
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (758)
GSM3443369 E4.5-5.5_new_Plate1_A02 (scBS-Seq)
GSM3443370 E4.5-5.5_new_Plate1_A03 (scBS-Seq)
GSM3443371 E4.5-5.5_new_Plate1_A04 (scBS-Seq)
This SubSeries is part of SuperSeries:
GSE121708 Multi-omics profiling of mouse gastrulation at single cell resolution
Reanalyzed by GSE171332
BioProject PRJNA498125
SRA SRP166661

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE121690_RAW.tar 20.6 Gb (http)(custom) TAR (of TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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