Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic reconstruction of molecular cascades regulating growth plate development using single-cell RNA-seq

ABSTRACT: The growth plate, which comprises sequentially differentiated cell layers, is a critical structure for bone elongation and regeneration. Although several key regulators in growth plate development have been identified using primarily genetic perturbation, the systematic understanding is still limited. Here we used single cell RNA-seq to interrogate gene expression profiles of 217 single cells from growth plates, and developed the bioinfromatics pipeline Sinova to de-novo reconstruct physiological growth plate development in both temporal and spatial high-resolution. Our unsupervised model not only confirmed prior knowledge but also enabled systematic discovery of novel genes, potential signal pathways and surface markers CD9/CD200 to precisely depict the development. Sinova further identified effective transcriptional factor portfolio directing growth plate maturation, which was cross-validated experimentally using an in-vitro EGFP-Col10a screening system. Our case demonstrated systematic reconstructing of molecular cascades of a developmental process from single-cell profiling, and the workflow is readily transferable to other physiological scenarios.

ORGANISM(S): Mus musculus

PROVIDER: GSE76157 | GEO | 2016/06/14

SECONDARY ACCESSION(S): PRJNA306493

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Systematic reconstruction of molecular cascades regulating growth plate development using single-cell RNA-seq

Project description:The growth plate, which comprises sequentially differentiated cell layers, is a critical structure for bone elongation and regeneration. Although several key regulators in growth plate development have been identified using primarily genetic perturbation, the systematic understanding is still limited. Here we used single cell RNA-seq to interrogate gene expression profiles of 217 single cells from growth plates, and developed the bioinfromatics pipeline Sinova to de-novo reconstruct physiological growth plate development in both temporal and spatial high-resolution. Our unsupervised model not only confirmed prior knowledge but also enabled systematic discovery of novel genes, potential signal pathways and surface markers CD9/CD200 to precisely depict the development. Sinova further identified effective transcriptional factor portfolio directing growth plate maturation, which was cross-validated experimentally using an in-vitro EGFP-Col10a screening system. Our case demonstrated systematic reconstructing of molecular cascades of a developmental process from single-cell profiling, and the workflow is readily transferable to other physiological scenarios. 217 single-cell RNA-seq for cell isolated from mouse growth plate at postnatal day7

2016-06-14 | E-GEOD-76157 | biostudies-arrayexpress

Mus musculus

Project description:Systematic reconstruction of molecular cascades regulating growth plate development using single-cell RNA-seq

| PRJNA306493 | ENA

Systematic mapping of cell state trajectories, cell lineage, and perturbations in the zebrafish embryo using single cell transcriptomics

Project description:High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here, we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (“TracerSeq”) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin-deficient embryos. We provide web-based resources for further analysis of the single-cell data.

2018-04-26 | GSE112294 | GEO

Effect of different hydrostatic pressures on mouse metatarsal and hip cartilage tissues

Project description:Chondrocytes are subject to continuous loads placed upon them throughout development and physical activity. Normal physiological loads enable the maintenance of the articular cartilage health, however abnormal loads contribute to pathological joint ageing. Similarly, the growth plate cartilage is exposed to a number of loads during growth and development. Due to the high-water content of cartilage, hydrostatic pressure is considered one of the main biomechanical influences on chondrocytes and it plays an important role in the mechanoregulation of cartilage. Therefore in this study we conducted RNA-seq analysis of ex vivo hip cap (articular) and metatarsal (growth) cartilage cultures after physiological and injurious hydrostatic pressure. Gene expression in response to 5mPa (physiological) or 50mPa (injurious) hydrostatic pressure was quantified by transcriptome analysis using the Illumina platform

2023-12-27 | GSE234112 | GEO

Single-cell RNA-seq with Waterfall Reveals Molecular Cascades underlying Adult Hippocampal Neurogenesis

Project description:Somatic stem cells contribute to tissue ontogenesis, homeostasis, and regeneration through sequential processes. Systematic molecular analysis of stem cell behavior is challenging because classic approaches cannot resolve cellular heterogeneity or capture developmental dynamics. Here we provide a comprehensive resource of single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny. We further developed Waterfall, a bioinformatic suite, to statistically quantify singe-cell gene expression along de novo reconstructed continuous developmental trajectory. Our study reveals molecular signatures of qNSCs, characterized by high niche signaling integration and low protein translation capacity. Our analyses further delineate molecular cascades underlying adult qNSC activation and neurogenesis initiation, exemplified by decreased extrinsic signaling capacity, primed translational machinery, and regulatory switches in transcription factors, metabolism, and energy sources. Our study reveals the molecular continuum underlying adult neurogenesis and illustrates how Waterfall can be used for single-cell omics analyses of various continuous biological processes. Single-cell transcriptomes of adult hippocampal quiescent neural stem cells (qNSCs) and their immediate progeny.

2015-08-30 | E-GEOD-71485 | biostudies-arrayexpress

Hnrnpk orchestrates embryonic growth plate development via regulating glycolysis

Project description:Hnrnpk orchestrates embryonic growth plate development via regulating glycolysis

| PRJNA809664 | ENA

HGPC, in monolayer, 0.5 vs. 20% serum

Project description:Human growth plate chondrocytes were isolated from the distal femoral growth plate from a single adolescent undergoing epiphysiodesis. Cell were isolated and grown in monolayers, long term. Cells were replated and cultured in 0.5% or 20% serum. Keywords: parallel sample

2004-04-13 | GSE1277 | GEO

Single cell RNAseq analysis of Col2a1+ growth plate chondrocytes

Project description:Single cell RNAseq analysis of Col2a1+ growth plate chondrocytes

| PRJNA516448 | ENA

Single cell RNAseq analysis of Col2a1+ growth plate chondrocytes

Project description:We set out to reveal single cell transcriptional profiles of neonatal growth plate chondrocytes

2019-01-23 | GSE125464 | GEO

Single cell RNAseq analysis of murine fetal growth plate chondrocytes and perichondrial cells

Project description:We revealed a single cell transcriptional landscape of fetal growth plate chondrocytes and perichondrial cells.

2019-02-26 | GSE126966 | GEO