Single cell RNA sequence discover the musculoskeletal tissue cell atlas during limb development
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA427820 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10409200_1.fastq.gz | Fastqsanger.gz | |||
| SRR10409200_2.fastq.gz | Fastqsanger.gz | |||
| SRR10409300_1.fastq.gz | Fastqsanger.gz | |||
| SRR10409300_2.fastq.gz | Fastqsanger.gz | |||
| SRR10409400_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 4160 |
Similar Datasets
Project description:By using single cell RNA-seq,We dissect the cellular heterogeneity and transcriptome profiles during limb development, and reveal the characteristic features of limb development and musculoskeletal stem/progenitor cell populations involved in limb lineage development. Our study therefore systematically decoded molecular markers and cellular program of limb development that would shed lights on limb developmental biology.
2020-12-28 | GSE108612 | GEO
Project description:26 limb-girdle muscular dystrophy patients from Latvia and 34 patients from Lithuania with clinical symptoms of limb-girdle muscular dystrophies, along with 204 healthy unrelated controls were genotyped for 96 most frequent known limb-girdle muscular dystrophies causing mutations for the region, using VeraCode GoldenGate system. More information can be found in article Robust genotyping tool for autosomal recessive type of limb-girdle muscular dystrophies in BMC Musculoskeletal Disorders by I. Inashkina et al.
2016-04-28 | E-MTAB-4662 | biostudies-arrayexpress
Project description:Humans and other tetrapods are considered to require apical-ectodermal-ridge, AER, cells for limb development, and AER-like cells are suggested to be re-formed to initiate limb regeneration. Paradoxically, the presence of AER in the axolotl, the primary regeneration model organism, remains controversial. Here, by leveraging a single-cell transcriptomics-based multi-species atlas, composed of axolotl, human, mouse, chicken, and frog cells, we first established that axolotls contain cells with AER characteristics. Surprisingly, further analyses and spatial transcriptomics revealed that axolotl limbs do not fully re-form AER cells during regeneration. Moreover, the axolotl mesoderm displays part of the AER machinery, revealing a novel program for limb (re)growth. These results clarify the debate about the axolotl AER and the extent to which the limb developmental program is recapitulated during regeneration.
2023-09-20 | GSE243225 | GEO
Project description:Limb development has long served as a model system for studying how a pool of progenitor cells undergoes coordinated spatial patterning and differentiation to produce complex and well-organized structures. Here, we identify a population of naïve-state limb progenitors and show that they differentiate progressively to form the skeleton in a complex nonconsecutive three-dimensional pattern. First, by performing single-cell RNA sequencing of the developing mouse forelimb we created an atlas of cellular compositions and transcriptional states. This atlas revealed three progenitor states: naïve, proximal and autopodial, as well as Msx1 as a marker for the naïve progenitors. In vivo lineage tracing analysis firmly established this role of Msx1 and localized the naïve progenitors to the outer margin of the developing limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that Msx1 naïve progenitors undergo progressive and simultaneous transition into both proximal and autopodial progenitors and then to Sox9+ chondroprogenitors. Interestingly, the progressive differentiation to chondroprogenitors occurred along all the skeletal segments concurrently, suggesting that skeleton form in a nonconsecutive way. Indeed, by tracking the spatiotemporal sequence of naïve progenitor differentiation, we found that the skeleton forms in a complex nonconsecutive three-dimensional pattern. Overall, these findings propose a new model for limb skeleton development. Limb development has long served as a model system for studying how a pool of progenitor cells undergoes coordinated spatial patterning and differentiation to produce complex and well-organized structures. Here, we identify a population of naïve-state limb progenitors and show that they differentiate progressively to form the skeleton in a complex nonconsecutive three-dimensional pattern. First, by performing single-cell RNA sequencing of the developing mouse forelimb we created an atlas of cellular compositions and transcriptional states. This atlas revealed three progenitor states: naïve, proximal and autopodial, as well as Msx1 as a marker for the naïve progenitors. In vivo lineage tracing analysis firmly established this role of Msx1 and localized the naïve progenitors to the outer margin of the developing limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that Msx1 naïve progenitors undergo progressive and simultaneous transition into both proximal and autopodial progenitors and then to Sox9+ chondroprogenitors. Interestingly, the progressive differentiation to chondroprogenitors occurred along all the skeletal segments concurrently, suggesting that skeleton form in a nonconsecutive way. Indeed, by tracking the spatiotemporal sequence of naïve progenitor differentiation, we found that the skeleton forms in a complex nonconsecutive three-dimensional pattern. Overall, these findings propose a new model for limb skeleton development. Limb development has long served as a model system for studying how a pool of progenitor cells undergoes coordinated spatial patterning and differentiation to produce complex and well-organized structures. Here, we identify a population of naïve-state limb progenitors and show that they differentiate progressively to form the skeleton in a complex nonconsecutive three-dimensional pattern. First, by performing single-cell RNA sequencing of the developing mouse forelimb we created an atlas of cellular compositions and transcriptional states. This atlas revealed three progenitor states: naïve, proximal and autopodial, as well as Msx1 as a marker for the naïve progenitors. In vivo lineage tracing analysis firmly established this role of Msx1 and localized the naïve progenitors to the outer margin of the developing limb, along the anterior-posterior axis. Sequential pulse-chase experiments showed that Msx1 naïve progenitors undergo progressive and simultaneous transition into both proximal and autopodial progenitors and then to Sox9+ chondroprogenitors. Interestingly, the progressive differentiation to chondroprogenitors occurred along all the skeletal segments concurrently, suggesting that skeleton form in a nonconsecutive way. Indeed, by tracking the spatiotemporal sequence of naïve progenitor differentiation, we found that the skeleton forms in a complex nonconsecutive three-dimensional pattern. Overall, these findings propose a new model for limb skeleton development.
2023-01-17 | GSE185940 | GEO
Project description:Detailed information about stage-specific changes in gene expression is crucial for understanding the gene regulatory networks underlying development and the various signal transduction pathways contributing to morphogenesis. Here, we describe the global gene expression dynamics during early murine limb development, when cartilage, tendons, muscle, joints, vasculature, and nerves are specified and the musculoskeletal system of the limbs is established. We used whole-genome microarrays to identify genes with differential expression at 5 stages of limb development (E9.5 to 13.5), during fore-limb and hind-limb patterning. We found that the onset of limb formation is characterized by an up-regulation of transcription factors, which is followed by a massive activation of genes during E10.5 and E11.5 which tampers off at later time points. Among 3520 genes identified as significantly up-regulated in the limb, we find ~30% to be novel, dramatically expanding the repertoire of candidate genes likely to function in the limb. Hierarchical and stage-specific clustering identified expression profiles that correlate with functional programs during limb development and are likely to provide new insights into specific tissue patterning processes. Here we provide for the first time, a comprehensve analysis of developmentally regulated genes during murine limb development, and provide some novel insights into the expression dynamics governing limb morphogenesis. Fifty- one arrays were analyzed, consisting of whole fore-limb and hind-limb bud RNA (experimental) and whole embryo RNA (reference) samples from E9.5 to E13.5 DPC mouse (FVB strain). Embryos were not pooled to generate samples. Each time point has 3 to 5 biological replicates for limb bud samples, duplicates for whole embryos. Comparisons were made between limb bud samples and whole embryo at the same stage, fore-limb samples of different stages, hind-limb samples of different stages, and fore-limb samples compared to hind-limb samples at the same or the next stage.
2011-12-31 | E-GEOD-30138 | biostudies-arrayexpress
Project description:Aberrant repair after musculoskeletal injury is one of the most costly and common clinical scenarios in health care. While advances in our understanding of the key cells and pathways during the repair process have improved, there remains a gap in knowledge of the key progenitor cells and their interaction with the surrounding microenvironment. Heterotopic ossification (HO) is a pathological process caused by aberrant cell-fate determination resulting in the formation of bone in non-skeletal tissues after musculoskeletal injury. While the involvement of blood vessels in musculoskeletal repair is well-documented, the role of lymphatic vessels and the cells responsible for their ingrowth in musculoskeletal tissues during both homeostasis and after injury remains poorly understood. In this study, we employed a mouse model of traumatic HO to investigate lymphangiogenesis during musculoskeletal injury and repair and to uncover the key progenitor cells responsible to stimulate lymphangiogenesis and undergo aberrant cell fate differentiation. Our findings demonstrated that musculoskeletal injury triggered lymphangiogenesis at the injury site, including invasion of lymphatic vessels into the tendon proper. This increased lymphangiogenesis was driven by elevated levels of active Vascular Endothelial Growth Factor C (VEGF-C) one-week post-injury. Through single-cell transcriptomic analyses, we identified mesenchymal progenitor cells (MPCs) as a source of Vegfc following injury as well as the source of enzymes responsible for activating VEGF-C. These Vegfc-expressing MPCs underwent osteochondral differentiation and actively contributed to the formation of HO following injury. Notably, Vegfc haploinsufficiency resulted in a near 50% reduction in lymphangiogenesis and HO formation. Collectively, these findings suggest that MPC expression of VEGF-C and its activating enzymes in response to soft tissue trauma play a critical role in stimulating pathologic lymphatic vessel growth. Furthermore, Vegfc expressing MPCs undergo aberrant osteochondral differentiation responsible for HO. Targeting Vegfc expression and Vegfc-expressing progenitors therapeutically could potentially mitigate pathologic lymphangiogenesis, preventing aberrant tissue repair and subsequent HO formation.
2024-06-13 | GSE255500 | GEO
Project description:Multi-species atlas resolves an axolotl limb development and regeneration paradox
| PRJNA1017433 | ENA
Project description:Detailed information about stage-specific changes in gene expression is crucial for understanding the gene regulatory networks underlying development and the various signal transduction pathways contributing to morphogenesis. Here, we describe the global gene expression dynamics during early murine limb development, when cartilage, tendons, muscle, joints, vasculature, and nerves are specified and the musculoskeletal system of the limbs is established. We used whole-genome microarrays to identify genes with differential expression at 5 stages of limb development (E9.5 to 13.5), during fore-limb and hind-limb patterning. We found that the onset of limb formation is characterized by an up-regulation of transcription factors, which is followed by a massive activation of genes during E10.5 and E11.5 which tampers off at later time points. Among 3520 genes identified as significantly up-regulated in the limb, we find ~30% to be novel, dramatically expanding the repertoire of candidate genes likely to function in the limb. Hierarchical and stage-specific clustering identified expression profiles that correlate with functional programs during limb development and are likely to provide new insights into specific tissue patterning processes. Here we provide for the first time, a comprehensve analysis of developmentally regulated genes during murine limb development, and provide some novel insights into the expression dynamics governing limb morphogenesis.
2011-12-31 | GSE30138 | GEO