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Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [BS-seq]

ABSTRACT: Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [BS-seq]

PROVIDER: PRJNA563326 | ENA |

REPOSITORIES: ENA

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Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [BS-seq]

Project description:In mammals, drastic epigenomic reprogramming occurs during preimplantation development. However, the functional associations between different epigenetic layers and transcriptional regulation remains unclear, and to what extent, the dynamic epigenomics contribute to the lineage segregation remains to be elucidated. Here, we developed a single cell multi-omics sequencing technology, and provided the first single cell multi-comics map of chromatin accessibility, DNA methylation and RNA transcription during mouse preimplantation development.

2021-01-12 | GSE136716 | GEO

Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing

Project description:Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing

| PRJNA563322 | ENA

Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [NOME-seq]

Project description:Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [NOME-seq]

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Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [RNA-seq]

Project description:Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [RNA-seq]

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Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [NOME-seq]

2021-01-12 | GSE136715 | GEO

Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [RNA-seq]

2021-01-12 | GSE136714 | GEO

Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-01-12 | GSE136718 | GEO

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

Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restrict differentiation into distinct fates

Project description:One of the keys to achieving skin regeneration lies within understanding the heterogeneity of neonatal fibroblasts, which support skin regeneration. However, the molecular underpinnings regulating the cellular states and fates of these cells are not fully understood. To investigate this, we performed a parallel multi-omics analysis by processing neonatal murine skin for single-cell ATAC-sequencing (scATAC-seq) and single-cell RNA-sequencing (scRNA-seq) separately. Our approach revealed that fibroblast clusters could be sorted into papillary and reticular lineages based on transcriptome profiling, as previously published. However, scATAC-seq analysis of neonatal fibroblast lineage markers, such as, Dpp4/CD26, Corin, and Dlk1 along with markers of myofibroblasts, revealed accessible chromatin in all fibroblast populations despite their lineage specific transcriptome profiles. These results suggests that accessible chromatin does not always translate to gene expression and that many fibroblast lineage markers reflect a fibroblast state, which includes neonatal papillary, reticular, and myofibroblasts. This analysis also provides a possible explanation as to why these marker genes can be promiscuously expressed in different fibroblast populations under different conditions. Our scATAC-seq analysis also revealed that the functional lineage restriction between dermal papilla and adipocytes fates are regulated by distinct chromatin landscapes. Finally, we have developed a webtool for our multi-omics analysis: https://skinregeneration.org/scatacseq-and-scrnaseq-data-from-thompson-et-al-2021-2/.

2021-11-24 | GSE189210 | GEO

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

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