Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omics profiling of mouse gastrulation at single cell resolution

ABSTRACT: Multi-omics profiling of mouse gastrulation at single cell resolution

PROVIDER: PRJNA498124 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8091080_1.fastq.gz	Fastqsanger.gz
	SRR8091080_2.fastq.gz	Fastqsanger.gz
	SRR8091090_1.fastq.gz	Fastqsanger.gz
	SRR8091090_2.fastq.gz	Fastqsanger.gz
	SRR8091100_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9662

Similar Datasets

Multi-omics profiling of mouse gastrulation at single-cell resolution.

Project description:Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan and is associated with major transcriptional changes1-5. Global epigenetic reprogramming accompanies these changes6-8, but the role of the epigenome in regulating early cell-fate choice remains unresolved, and the coordination between different molecular layers is unclear. Here we describe a single-cell multi-omics map of chromatin accessibility, DNA methylation and RNA expression during the onset of gastrulation in mouse embryos. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements at enhancer marks, driven by ten-eleven translocation (TET)-mediated demethylation and a concomitant increase of accessibility. By contrast, the methylation and accessibility landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or remodelled before cell-fate decisions, providing the molecular framework for a hierarchical emergence of the primary germ layers.

| S-EPMC6924995 | biostudies-literature

Single Cell Multi-Omics Profiling Using ISSAAC-seq

Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.

2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress

High spatial resolution multi-omics atlas sequencing of mouse embryos

Project description:Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.

2020-09-16 | GSE137986 | GEO

Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at the single-cell level

Project description:We use multi-omics (ATAC-seq, single cell RNA-seq and differential bulk RNA-seq) to increase resolution of the sea urchin posterior gut GRN for the cells expressing the ParaHox gene Sp-Pdx1.

2024-08-06 | GSE262916 | GEO

A multi-omics atlas of the human retina at single-cell resolution

Project description:Cell types in the human retina are highly heterogeneous with their abundance varies by several orders of magnitude. To decipher the complexity of gene expression and regulation of the human retinal cell types, we generated a multi-omics single-cell atlas of the adult human retina, including over 250K nuclei for single-nuclei RNA-seq and 150K nuclei for single-nuclei ATAC-seq. Over 60 cell subtypes have been identified based on their transcriptomic profiles, reaching a sensitivity of 0.01%. Integrative analysis of this single-cell multi-omics dataset identified gene regulatory elements across the genome for each cell subtype. In addition, when combined with other data modalities, such as eQTL, potential causal variants can be identified through fine mapping. Taken together, this new dataset represents the most comprehensive single-cell multi-omics profiling for the human retina that enables in-depth molecular characterization of most cell subtypes.

2023-03-14 | GSE226108 | GEO

Multi-omics profiling of mouse gastrulation at single cell resolution

Project description:This SuperSeries is composed of the SubSeries listed below. Useful links: Parsed data: (ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation) Github repository: (https://github.com/rargelaguet/scnmt_gastrulation)

2019-09-30 | GSE121708 | GEO

A multi-omics atlas of the human retina at single-cell resolution

Project description:A multi-omics atlas of the human retina at single-cell resolution

| PRJNA938514 | ENA

High spatial resolution multi-omics atlas sequencing of mouse embryos

Project description:High spatial resolution multi-omics atlas sequencing of mouse embryos

| PRJNA574105 | ENA

Single-cell Multi-omics Sequencing and Analyses of Human Colorectal Cancer

Project description:Although genomic instability, epigenetic abnormality, and gene expression dysregulation are hallmarks of colorectal cancer, these features have not been simultaneously analyzed at single-cell resolution. Using optimized single-cell multi-omics sequencing together with multi-regional sampling of the primary tumor, lymphatic and distant metastases, we provide insights beyond intratumoral heterogeneity. Genome-wide DNA methylation levels were relatively consistent within a single genetic sub-lineage. The genome-wide DNA demethylation patterns of cancer cells were consistent in all 10 sequenced patients. Our work demonstrates the feasibility of reconstructing genetic lineages, and tracing their epigenomic and transcriptomic dynamics with single-cell multi-omics sequencing.

2018-11-29 | GSE97693 | GEO

Single cell multi-omics profiling of H3-K27M DMG

Project description:Multi-omics profiling of H3-K27M DMGs across different age groups and locations, using fresh single whole cell RNA-seq, scATACseq, spatial in situ sequencing, and WES/targeted exome sequencing.

2022-08-09 | GSE184357 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data