About: The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: The changing mouse embryo transcriptome at whole tissue and single-cell resolution Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The changing mouse embryo transcriptome at whole tissue and single-cell resolution
Creator	Zhang, Yu Williams, Brian Amrhein, Henry Dickel, Diane Goh, Say-Tar Hardison, Ross Pennacchio, Len Ren, Bing Trout, Diane Visel, Axel Wold, Barbara Afzal, Veena Berghella, Libera He, Peng Marinov, Georgi Plajzer-Frick, Ingrid
Source	PMC
abstract	During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system(1). Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.
has issue date	2020-07-29(xsd:dateTime)
bibo:doi	10.1038/s41586-020-2536-x
bibo:pmid	32728245
has license	cc-by
sha1sum (hex)	a963a10bb07f2a0e25439af526437ca3c27afa71
schema:url	https://doi.org/10.1038/s41586-020-2536-x
resource representing a document's title	The changing mouse embryo transcriptome at whole tissue and single-cell resolution
has PubMed Central identifier	PMC7410830
has PubMed identifier	32728245
schema:publication	Nature
resource representing a document's body	covid:a963a10bb07f2a0e25439af526437ca3c27afa71#body_text
is schema:about of	named entity 'cell types' named entity 'day' named entity 'identified' named entity 'integrate' named entity 'reference data' named entity 'companion' named entity 'differential' named entity 'clusters' named entity 'sets' named entity 'mouse' named entity 'EXTRACTED' named entity 'DEVELOPMENTAL' named entity 'INCLUDED' named entity 'RNA DATA' named entity 'MORE THAN' named entity 'RELATIONSHIPS' named entity 'Here' named entity 'promoters' named entity 'codes' named entity 'companion' named entity 'differentiating' named entity 'mouse' named entity 'structured' named entity 'transcriptome' named entity 'sequencing' named entity 'data' named entity 'transcription factor' named entity 'dynamic' named entity 'limb' named entity 'tissue' named entity 'single-cell' named entity 'ENCODE' named entity 'organ' named entity 'sequencing of RNA' named entity 'mammalian embryogenesis' named entity 'differential gene expression' named entity 'embryonic development' named entity 'reverse transcribed' named entity 'transcriptome' named entity 'transcription factor' named entity '10.5' named entity 'embryo' named entity 'FANTOM' named entity 'database' named entity 'cell types' named entity 'PCA' named entity 'Pearson correlation' named entity 'haematopoetic' named entity 'EMPs' named entity 'RNA' named entity 'H3K27me3' named entity 'transcriptome' named entity 'mesoderm' named entity 'stochastic' named entity 'sample variance' named entity 'repressors' named entity 'tRNA' named entity 'histogenesis' named entity 'DNA motif' named entity 'single-cell data' named entity 'sample matrix' named entity 'scRNA-seq' named entity 'histogenesis' named entity 'embryo' named entity 'cell-type' named entity 'scRNA-seq'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software