ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

García-Castro, Helena; Kenny, Nathan J.; Iglesias, Marta; Álvarez‐Campos, Patricia; Mason, Vincent; Elek, Anamaria; Schönauer, Anna; Sleight, Victoria A.; Neiro, Jakke; Aboobaker, A. Aziz; Permanyer, Jon; Irimia, Manuel; Sebé-Pedrós, Arnau; Solana, Jordi

doi:10.1186/s13059-021-02302-5

Cited by 63 publications

(105 citation statements)

References 82 publications

(72 reference statements)

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“…We carried out separate ACME dissociations for each developmental stage (Fig 1B) [3]. ACME allowed early fixation of cells and therefore reduced the stress responses that occur with enzymatic dissociations.…”

Section: Resultsmentioning

confidence: 99%

“…Here we have also taken advantage of our recent advances in cell dissociation, combining ACetic-MEthanol (ACME) dissociation [3] and the SPLiT-seq scRNA-seq [59] technology to describe at cellular resolution spider embryogenesis at stages 7, 8 and 9. This has allowed us to define cell types and capture new candidate genes involved in several important developmental processes during these key stages of embryogenesis.…”

Section: Introductionmentioning

confidence: 99%

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An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Leite

Schoenauer

Blakeley

et al. 2022

Preprint

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Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis has made important contributions to understanding the evolution of animal development. In particular, studies of the common house spider Parasteatoda tepidariorum using developmental candidate gene approaches have provided key insights into the regulation and evolution of many processes including axis formation, segmentation and patterning. However, there remains a paucity of knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 23 cell clusters marked by many developmental toolkit genes, as well as a plethora of non-candidate genes not previously investigated. We found many Hox genes were markers of cell clusters, and Hox gene paralogs often were present in different clusters. This provided further evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in the arachnopulmonate ancestor. We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and the evolution of these processes among animals at cellular resolution.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Leite

Schoenauer

Blakeley

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Furthermore, the analysis of single-cell gene expression variations in the special context of tissue is also a crucial perspective in the development of scRNA-seq technology, since the spatial variations of transcriptomic expressions in single cells throughout certain tissues are important evidence to unravel how cellular expressions change in response to the presence and proximity to other cells (Ståhl et al, 2016). The spacial analysis could be achieved by gene expression patterning technologies such as the application of in situ hybridization (ISH) or fluorescence in situ hybridization (FISH) to highlight marker genes and visualize cell morphology and gene expression locations (Horie et al, 2018;Soria et al, 2020;Chari et al, 2021;Garcıá-Castro et al, 2021). New techniques merging scRNA-seq and marker gene localization (e.g., spatial transcriptome techniques like SeqFISH+ and VISIUM) are urgently needed in the study of marine organisms (Ståhl et al, 2016;Longo et al, 2021).…”

Section: Future Directions Of Single-cell Sequencing On Marine Organismsmentioning

confidence: 99%

Single-Cell Sequencing on Marine Life: Application and Future Development

Wang

2022

Front. Mar. Sci.

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Single-cell RNA-sequencing (scRNA-seq) is the genomic approach that directly examines gene expression information from individual cells and provides a higher resolution of cellular differences than bulk RNA-seq. In the past decade, with the rapid development of microfluid, barcoding, and next-generation sequencing (NGS) technologies, scRNA-seq has revolutionized transcriptomic studies and gained great success and broad prospects. However, compared with the wide use in the few model animals, the application of scRNA-seq in marine organisms is limited due to the high cost of early scRNA-seq and the immature of single-cell methods for marine organisms. Recently, with the increase of genomic data, maturation of scRNA-seq platform and downstream bioinformatics algorithms, the scRNA-seq has been successfully applied in several marine model animals with great success, which demonstrated that the scRNA-seq could be the ideal and powerful tool to extend our understanding of marine organisms’ evolutionary and physiological processes and their adaptation to ecological niches. Here, we review the state-of-the-art improvements of single-cell sequencing techniques and new studies that apply single-cell methods to marine organisms. We also summarize the opportunities and challenges scientists may face in further single-cell research and propose several appealing prospects that may benefit from the combination of single-cell techniques and marine organisms.

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“…In addition, some studies have already shown the role that the epigenetic regulation and chromatin remodeling has on neoblasts maintenance and differentiation and will become another important field of study in the near future. Finally, the development of novel tools such as ACME maceration [151] that will allow for a better characterization of planarian cell types and lineages will definitely help to advance in our knowledge on how neoblasts drive regeneration in these amazing animals.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Decoding Stem Cells: An Overview on Planarian Stem Cell Heterogeneity and Lineage Progression

Molina

Cebrià

2021

Biomolecules

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Planarians are flatworms capable of whole-body regeneration, able to regrow any missing body part after injury or amputation. The extraordinary regenerative capacity of planarians is based upon the presence in the adult of a large population of somatic pluripotent stem cells. These cells, called neoblasts, offer a unique system to study the process of stem cell specification and differentiation in vivo. In recent years, FACS-based isolation of neoblasts, RNAi functional analyses as well as high-throughput approaches such as single-cell sequencing have allowed a rapid progress in our understanding of many different aspects of neoblast biology. Here, we summarize our current knowledge on the molecular signatures that define planarian neoblasts heterogeneity, which includes a percentage of truly pluripotent stem cells, and guide the commitment of pluripotent neoblasts into lineage-specific progenitor cells, as well as their differentiation into specific planarian cell types.

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ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

Cited by 63 publications

References 82 publications

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Single-Cell Sequencing on Marine Life: Application and Future Development

Decoding Stem Cells: An Overview on Planarian Stem Cell Heterogeneity and Lineage Progression

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