sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing.

Typical high-throughput single-cell RNA-sequencing (scRNA-seq) analyses are primarily conducted by (pseudo)alignment, through the lens of annotated gene models, and aimed at detecting differential gene expression. This misses diversity generated by other mechanisms that diversify the transcriptome such as splicing and V(D)J recombination, and is blind to sequences missing from imperfect reference genomes. Here, we present sc-SPLASH, a highly efficient pipeline that extends our SPLASH framework for statistics-first, reference-free discovery to barcoded scRNA-seq (10x Chromium) and spatial transcriptomics (10x Visium); we also provide its optimized module for preprocessing and -mer counting in barcoded data, BKC, as a standalone tool.

Methods for cell isolation and analysis of the highly regenerative tunicate .

is the only molecularly characterized solitary ascidian capable of regenerating all organs and tissue types. The cellular basis for regeneration in is largely unknown, and methods for isolating live cells from this species for functional analyses are unavailable. Here, we developed a method for isolating live cells from , overcoming major experimental challenges, including the dissociation of its thick body wall and native cellular autofluorescence.

Stemness Activity Underlying Whole Brain Regeneration in a Basal Chordate.

Understanding how neurons regenerate following injury remains a central challenge in regenerative medicine. Adult mammals have a very limited ability to regenerate new neurons in the central nervous system (CNS). In contrast, the basal chordate can regenerate its entire CNS within seven days of complete removal.

Molecular characterization of the immediate wound response of the solitary ascidian Polycarpa mytiligera.

Background: Injury response is key to successful regeneration. Yet, transcriptome analyses of injury response were performed only on a handful of regenerative organisms. Here, we studied the injury response of the solitary ascidian Polycarpa mytiligera, an emerging model system, capable of regenerating any body part.

And Then There Were Three…: Extreme Regeneration Ability of the Solitary Chordate .

Extensive regenerative ability is a common trait of animals capable of asexual development. The current study reveals the extraordinary regeneration abilities of the solitary ascidian . Dissection of a single individual into separate fragments along two body axes resulted in the complete regeneration of each fragment into an independent, functional individual.

Spawning induction, development and culturing of the solitary ascidian , an emerging model for regeneration studies.

Background: Ascidians (phylum Chordata, class Ascidiacea) represent the closest living invertebrate relatives of the vertebrates and constitute an important model for studying the evolution of chordate development. The solitary ascidian exhibits a robust regeneration ability, unique among solitary chordates, thus offering a promising new model for regeneration studies. Understanding its reproductive development and establishing land-based culturing methods is pivotal for utilizing this species for experimental studies.

Solitary Ascidians as Model Organisms in Regenerative Biology Studies.

Regeneration, the process of replacing lost or damaged body parts, has long captured human imagination and is a key feature among all animal phyla. Due to their close phylogenetic relationship to vertebrates and their high regenerative abilities, ascidians (Chordata, Ascidiacea) are often used as models to shed light on the cellular and genetic process involved in tissue regeneration. Surprisingly, ascidian regeneration studies are based on only a few model species.

Gut-spilling in chordates: evisceration in the tropical ascidian Polycarpa mytiligera.

The ejection of internal organs, i.e., evisceration, is a well-known phenomenon in sea-cucumbers.