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A Single-cell Transcriptomic Atlas of the Developing Chicken Limb
- Source :
- BMC Genomics, Vol 20, Iss 1, Pp 1-15 (2019), BMC Genomics
- Publication Year :
- 2019
- Publisher :
- Cold Spring Harbor Laboratory, 2019.
-
Abstract
- BackgroundThrough precise implementation of distinct cell type specification programs, differentially regulated in both space and time, complex patterns emerge during organogenesis. Thanks to its easy experimental accessibility, the developing chicken limb has long served as a paradigm to study vertebrate pattern formation. Through decades’ worth of research, we now have a firm grasp on the molecular mechanisms driving limb formation at the tissue-level. However, to elucidate the dynamic interplay between transcriptional cell type specification programs and pattern formation at its relevant cellular scale, we lack appropriately resolved molecular data at the genome-wide level. Here, making use of droplet-based single-cell RNA-sequencing, we catalogue the developmental emergence of distinct tissue types and their transcriptome dynamics in the distal chicken limb, the so-called autopod, at cellular resolution.ResultsUsing single-cell RNA-sequencing technology, we sequenced a total of 17,628 cells coming from three key developmental stages of chicken autopod patterning. Overall, we identified 23 cell populations with distinct transcriptional profiles. Amongst them were small, albeit essential populations like the apical ectodermal ridge, demonstrating the ability to detect even rare cell types. Moreover, we uncovered the existence of molecularly distinct sub-populations within previously defined compartments of the developing limb, some of which have important signaling functions during autopod pattern formation. Finally, we inferred gene co-expression modules that coincide with distinct tissue types across developmental time, and used them to track patterning-relevant cell populations of the forming digits.ConclusionsWe provide a comprehensive functional genomics resource to study the molecular effectors of chicken limb patterning at cellular resolution. Our single-cell transcriptomic atlas captures all major cell populations of the developing autopod, and highlights the transcriptional complexity in many of its components. Finally, integrating our data-set with other single-cell transcriptomics resources will enable researchers to assess molecular similarities in orthologous cell types across the major tetrapod clades, and provide an extensive candidate gene list to functionally test cell-type-specific drivers of limb morphological diversification.
- Subjects :
- 0106 biological sciences
Apical ectodermal ridge
Cell type
Candidate gene
lcsh:QH426-470
Organogenesis
lcsh:Biotechnology
Biology
Proteomics
01 natural sciences
Transcriptome
Autopod patterning
03 medical and health sciences
0302 clinical medicine
Perichondrium
lcsh:TP248.13-248.65
biology.animal
scRNA-seq
Digits
Interdigit
Genetics
Animals
Gene
Phalanges
Body Patterning
030304 developmental biology
0303 health sciences
Gene Expression Regulation, Developmental
Vertebrate
Extremities
lcsh:Genetics
Evolutionary biology
Cellular transcriptomics
Gene expression
Single-Cell Analysis
DNA microarray
Chickens
Functional genomics
030217 neurology & neurosurgery
Signal Transduction
Transcription Factors
Research Article
010606 plant biology & botany
Biotechnology
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- BMC Genomics, Vol 20, Iss 1, Pp 1-15 (2019), BMC Genomics
- Accession number :
- edsair.doi.dedup.....2117017089ed6ac1474bc7e0cde630e1
- Full Text :
- https://doi.org/10.1101/598227