Single cell transcriptomes of developing chicken hind limbs at stages HH25, HH29 and HH31
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE130439 | GEO | 2019/05/09
REPOSITORIES: GEO
Similar Datasets
Project description:We sequenced single cells coming from three developmental stages of chicken forelimb. We identified different cell populations with distinct transcriptional profiles. The supplementary file contains processed UMI count matrices, which also include meta data of each cell, e.g. cluster.
2021-05-18 | GSE174565 | GEO
Project description:Artiodactyls display skeletal adaptations for cursorial (running) locomotion. In these animals, the distal limb skeleton is symmetric, which facilitates walking on the tips of the two central digits, while lateral digits are reduced or lost. We have identified that one primary molecular alteration during the formation of the bovine limb is that, in contrast to mouse, the posterior limb bud mesenchyme does not upregulate Ptch1 expression in response to SHH. We have tracked down this dissimilarity to a cis-regulatory SHH-responsive element that is functionally altered in bovine and established a causal link between lack of upregulation of Ptch1 and acquisition of a symmetric distal autopod.
2014-06-19 | GSE52988 | GEO
Project description:Artiodactyls display skeletal adaptations for cursorial (running) locomotion. In these animals, the distal limb skeleton is symmetric, which facilitates walking on the tips of the two central digits, while lateral digits are reduced or lost. We have identified that one primary molecular alteration during the formation of the bovine limb is that, in contrast to mouse, the posterior limb bud mesenchyme does not upregulate Ptch1 expression in response to SHH. We have tracked down this dissimilarity to a cis-regulatory SHH-responsive element that is functionally altered in bovine and established a causal link between lack of upregulation of Ptch1 and acquisition of a symmetric distal autopod. A high resolution 4C-seq protocol involving two restriction digests was applied to viewpoint in Ptch1 promoter (mm9 chr13:63,667,995-63,669,157) in three different tissues, allowing robust detection of physical interactions between regulatory DNA elements.
2014-06-19 | E-GEOD-52988 | biostudies-arrayexpress
Project description:The free limb is subdivided into three anatomical domains along the proximodistal axis: the stylopod, zeugopod and autopod. These domains possess a specific number and pattern of the bones and each bone possesses unique morphology and length. During limb development, the mesenchymal cells of limb bud first forms precartilaginous aggregates which eventually grow and differentiate into the limb cartilage. Expression of Hox genes belonging to the Abd-B family, Hox9-13, is closely related to the anatomical domains of the limb bones and crucial for controlling morphogenesis and patterning of the limb cartilage. Hoxa13 and Hoxd13 are expressed in the autopodal mesenchyme and double KO mice have smaller autopods during the embryonic stage and a fan-shaped cartilage develops instead of the normal five digits. Thus, Hoxa13 and Hoxd13 are crucial for the cartilage patterning in the autopod. Since Hox encodes a transcription factor, Hox target genes function in region/compartment-specific formation of the precartilaginous condensation, cellular differentiation and proliferation of the cartilage. We used microarray to identified downstream genes of Hox13 in the autopod as exhibiting changes in the expression in the Hox13dKO mutant embryos.
2019-03-28 | GSE118640 | GEO
Project description:The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a ‘regulatory archipelago’ and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process. Transcriptional activity at the Hoxd locus in developing limbs and brain at E12.5
2011-11-28 | GSE31656 | GEO
Project description:Strigiformes are an order of raptorial birds consisting exclusively of owls: the Tytonidae (barn owls) and the Strigidae (true owls), united by a suite of adaptations aiding a keen predatory lifestyle, including robust hind limb elements modified for grip strength. To assess variation in hind limb morphology, we analysed how the dimensions of the major hind limb elements in subfossil and modern species scaled with body mass. Comparing hind limb element length, midshaft width, and robusticity index (RI: ratio of midshaft width to maximum length) to body mass revealed that femoral and tibiotarsal width scale with isometry, whilst length scales with negative allometry, and close to elastic similarity in the tibiotarsus. In contrast, tarsometatarsus width shows strong positive allometry with body mass, whilst length shows strong negative allometry. Furthermore, the tarsometatarsi RI scales allometrically to mass0.028, whilst a weak relationship exists in femora (mass0.004) and tibiotarsi (mass0.004). Our results suggest that tarsometatarsi play a more substantial functional role than tibiotarsi and femora. Given the scaling relationship between tarsometatarsal width and robusticity to body mass, it may be possible to infer the body mass of prehistoric owls by analysing tarsometatarsi, an element that is frequently preserved in the fossil record of owls.
| S-EPMC5361165 | biostudies-literature
Project description:In vitro models allow for the study of developmental processes outside of the embryo. To gain access to the cells mediating digit and joint development, we identified a unique property of undifferentiated mesenchyme isolated from the distal early autopod to autonomously re-assemble forming multiple autopod structures including: digits, interdigital tissues, joints, muscles and tendons. Single cell transcriptomic analysis of these developing structures revealed distinct cell clusters that express canonical markers of distal limb development including: Col2a1, Col10a1, and Sp7 (phalanx formation) Thbs2 and Col1a1, (perichondrium), Gdf5, Wnt5a, and Jun (joint interzone), Aldh1a2 and Msx1 (interdigital tissues), Myod1 (muscle progenitors), Prg4 (articular perichondrium/articular cartilage), and Scx and Tnmd (tenocytes/tendons). Analysis of the gene expression patterns for these signature genes indicates that developmental timing and tissue-specific localization were also recapitulated in a manner similar to the initiation and maturation of the developing murine autopod. Finally, the in vitro digit system also recapitulates congenital malformations associated with genetic mutations as in vitro cultures of Hoxa13 mutant mesenchyme produced defects present in Hoxa13 mutant autopods including digit fusions, reduced phalangeal segment numbers, and poor mesenchymal condensation. These findings demonstrate the robustness of the in vitro digit system to recapitulate digit and joint development. As an in vitro model of murine digit and joint development, this innovative system will provide access to developing limb tissues facilitating studies to discern how digit and articular joint formation is initiated and how undifferentiated mesenchyme is patterned to establish individual digit morphologies. The in vitro digit system also provides a platform to rapidly evaluate treatments aimed at stimulating the repair or regeneration of mammalian digits impacted by congenital malformation, injury, or disease.
2023-02-23 | GSE221883 | GEO
Project description:The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a ‘regulatory archipelago’ and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process. Chromosome Conformation Capture-on-chip analysis (4C) at the Hoxd locus in developing limbs and brain at E12.5
2011-11-28 | GSE31658 | GEO
Project description:The only freely flying mammals, bats, develop a pair of dramatically elongated hands and broad wing membranes. It is hypothesized that alterations of many gene expressions result in the bat wing formation. However, it remains to be proved. Here, by mRNA-seq, we found that hundreds of genes are significantly high expressed in the elongating forelimb digits. mRNA-seq data of 14 autopod samples from embryonic bats (Miniopterus schreibersii) were obtained by Illumina HiSeq 2000.
2014-04-14 | E-GEOD-50699 | biostudies-arrayexpress
Project description:We performed ChIP-seq for CTCF using the autopod from E12.5 embryo and confirmed the binding pattern previously reported by a ChIP-on-Chip approach using the same embryonic tissue (Soshnikova et al., 2010). Our results show CTCF-mediated gating of long-range contacts at the HoxD locus.
2017-07-12 | GSE96558 | GEO