Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1007779 | ENA |
REPOSITORIES: ENA
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Project description:Innate immune cells are a promising system for studying cell type evolution, as they are widespread across Metazoa, have several conserved functions, and are under selective pressure from pathogens. However, molecular characterizations of invertebrate immune cells are limited, and we do not know whether invertebrate immune cell types are homologous to those in vertebrates. Here we present a single-cell atlas of blood cells from a basal chordate, Ciona robusta, which lacks vertebrate innovations such as red blood cells and adaptive immunity. Using single-cell RNA sequencing, in situ hybridization, and live reporters, we extend definitions of C. robusta blood cells by showing that canonical, morphologically-defined cell types are transcriptomically heterogeneous. We find evidence that circulating blood contains a differentiation hierarchy with at least five major lineages. Mature blood cells include phagocytes, as well as over 20 cell states variously expressing vanadium-binding proteins, carbonic anhydrases, pattern recognition receptors, cytokines, and complement factors. Despite the expression of homologs to vertebrate immune components, we find that tunicate and vertebrate blood cell states share no clear homology in their transcriptomic profiles. Expression of transcription factors has also diverged. Altogether, this work modernizes blood cell classifications in C. robusta and reveals a surprising diversity of immune cells within chordates.
2025-05-23 | GSE296253 | GEO
Project description:Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.
2025-04-02 | GSE292926 | GEO
Project description:We used 10X Genomics Chromium system to profile single cells from a pool of Wild-type Ciona robusta embyros at 12 hours post fertilization (hpf)
2021-05-10 | GSE174127 | GEO
Project description:Ciona intestinalis (vase tunicate), kaCioInte3
| PRJNA1247553 | ENA
Project description:Styela clava transcriptome of embryos and larvae
| PRJNA523303 | ENA
Project description:The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.
2018-10-26 | GSE121807 | GEO