Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptional diversity is a hallmark of developmental potential

ABSTRACT: Single-cell transcriptional diversity is a hallmark of developmental potential

PROVIDER: PRJNA576262 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Single-cell transcriptional diversity is a hallmark of developmental potential

Project description:Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential—the number of expressed genes per cell—and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies (https://cytotrace.stanford.edu).

2020-01-28 | GSE138536 | GEO

Single-cell transcriptional diversity is a hallmark of developmental potential.

Project description:Single-cell RNA sequencing (scRNA-seq) is a powerful approach for reconstructing cellular differentiation trajectories. However, inferring both the state and direction of differentiation is challenging. Here, we demonstrate a simple, yet robust, determinant of developmental potential-the number of expressed genes per cell-and leverage this measure of transcriptional diversity to develop a computational framework (CytoTRACE) for predicting differentiation states from scRNA-seq data. When applied to diverse tissue types and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories. Additionally, it facilitated the identification of quiescent stem cells and revealed genes that contribute to breast tumorigenesis. This study thus establishes a key RNA-based feature of developmental potential and a platform for delineation of cellular hierarchies.

| S-EPMC7694873 | biostudies-literature

Post-transcriptional regulation in cranial neural crest cells expands developmental potential

Project description:Post-transcriptional regulation in cranial neural crest cells expands developmental potential

| PRJNA892136 | ENA

Post-transcriptional regulation in cranial neural crest cells expands developmental potential [II]

Project description:Post-transcriptional regulation in cranial neural crest cells expands developmental potential [II]

| PRJNA892142 | ENA

Post-transcriptional regulation in cranial neural crest cells expands developmental potential [I]

Project description:Post-transcriptional regulation in cranial neural crest cells expands developmental potential [I]

| PRJNA891631 | ENA

Developmental emergence of cortical neurogliaform cell diversity

Project description:GABAergic interneurons are key regulators of cortical circuit function. Among the dozens of reported transcriptionally distinct subtypes of cortical interneurons, neurogliaform cells (NGC) are unique: are recruited by long-range excitatory inputs and the primary source of slow cortical inhibition. Despite their functional importance, the developmental emergence and cellular diversity of NGCs remains unclear. Here, combining single-cell transcriptomics, genetic fate-mapping, electrophysiological morphological characterization, we reveal that discrete molecular subtypes of NGCs, with distinctive functional and anatomic profiles, populate the neocortex. Furthermore, we show that NGC subtypes emerge gradually through development, as incipient differential molecular signatures are apparent in Preoptic Area (POA) born NGC precursors. By identifying NGC developmentally-conserved transcriptional programs, we report that the transcription factor Tox2 constitutes an identity hallmark across NGC subtypes. Using CRISPR-Cas9-mediated genetic loss-of-function, we show that Tox2 is critical for NGC development: POA-born cells lacking Tox2 fail to differentiate into NGCs. Together, these results reveal that NGCs are born from a spatially restricted pool of Tox2+ POA precursors, after which intra-type diverging molecular programs are gradually acquired post-mitotically and result in functionally and molecularly discrete NGC cortical subtypes.

2023-06-30 | GSE225639 | GEO

Transcriptional disorganization of fibroblasts is a hallmark of the aging heart

Project description:Transcriptional disorganization of fibroblasts is a hallmark of the aging heart

| PRJEB32305 | ENA

Developmental emergence of cortical neurogliaform cell diversity

Project description:Developmental emergence of cortical neurogliaform cell diversity

| PRJNA936871 | ENA

Marsupial single-cell transcriptomics identifies temporal diversity in mammalian developmental programmes

Project description:Single-cell transcriptomics has demonstrated conserved and divergent programmes of organogenesis in mammals, but existing studies have focused on eutherians. Marsupials exhibit short gestation and complete development externally, necessitating accelerated differentiation of anterior features required for locomotion and feeding. Hence, they represent a unique outgroup for studying temporal shifts in development, known as heterochrony. Here, we generate a single-cell transcriptomic atlas of gastrulation and early organogenesis in a marsupial, the opossum Monodelphis domestica. We identify previously undocumented tissues undergoing heterochrony, and find that transcriptional programmes that form anterior structures initiate earlier and progress faster relative to eutherians. The result is uncoupling of transcriptional and morphological timelines, revealing unforeseen diversity in mammalian developmental sequences. Using our transcriptomic dataset, we identified translation as a candidate control mechanism by which anterior prioritisation is achieved. Our findings provide insight into the asynchronous progression of developmental programmes in marsupials.

2025-06-25 | GSE264385 | GEO

Transcriptional control of cone photoreceptor diversity by a thyroid hormone receptor

Project description:Purpose: To define the cone photoreceptor diversity and underlying transcriptional controls in mouse retina Methods: Individual retinal cone cells were isolated by micro-manipulator from dissociated pieces of superior/inferior retina from heterozygous (or homozygous) Thrb-b2Cre:Ai6 mice. Single cell libraries were constructed for RNA-seq analysis. Thrb-b2Cre;Rosa26-Sun1Gfp mice were used to isolate cone nuclei for ATAC-seq analysis. Thrb-HAB mice were used to identify TRb2 genomic binding sites using ChAP-seq analysis. Results: Developmental analyses of individual cones revealed a network of gradient genes. Many of these gradient genes are regulated by TRb2, a thyroid hormone receptor that has been associated with color visual impairment. Conclusions: The results suggest that TRb2 controls chromatin remodeling and transcriptional plasticity in the cone lineage to promote diversity.

2022-12-05 | GSE203481 | 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