Cell type diversity in the octopus brain
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA796958 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17606743_1.fastq.gz | Fastqsanger.gz | |||
| SRR17606743_2.fastq.gz | Fastqsanger.gz | |||
| SRR17606744_1.fastq.gz | Fastqsanger.gz | |||
| SRR17606744_2.fastq.gz | Fastqsanger.gz | |||
| SRR17606745_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 32 |
Similar Datasets
Project description:Octopuses are mollusks that evolved intricate neural systems which are comparable with vertebrates in terms of cell number, complexity and size. Exactly how an octopus increases its neural cell number so dramatically and whether an increase in cell type diversity enables higher cognitive function and complex behavior is still unknown. To profile the cell diversity of the developing octopus brain we applied 10x Genomics’ single-cell/nuclei RNA sequencing technology. At hatching, the Octopus vulgaris brain possesses the main lobes and connections of an adult brain, but which cell types are present remains elusive. We were able to identify 42 robust cell types comprising mostly neural cells, as well as multiple glial subtypes and other non-neuronal populations such as endothelial cells and fibroblasts. In situ expression analysis of marker genes allowed spatial mapping of clusters, including vertical lobe cells and several optic lobe cell types. Investigation of cell type conservation indicated similar gene expression signatures between glial cells of mice, fly and octopus. Genes related to memory and learning were found enriched in vertical lobe cells, that showed molecular similarities with Kenyon cells in Drosophila but not to any mouse cell type. Lastly, we also analyzed the expression of newly expanded gene families (protocadherins, C2H2 zinc-finger transcription factors and G-protein coupled receptors) and found that these are enriched in specific cell types. Taken together, our data gives insight into cell type evolution and the composition of the complex octopus brain.
2022-01-31 | GSE193622 | GEO
Project description:Cephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus- specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the “parts list” of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing.
2022-09-04 | GSE212528 | GEO
Project description:Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain cell types that control their sophisticated behavioral repertoire are still unknown. Here, we profile the cell diversity of the paralarval Octopus vulgaris brain to build a cell type atlas that comprises mostly neural cells, but also multiple glial subtypes, endothelial cells and fibroblasts. We spatially map cell types to the vertical, subesophageal and optic lobes. Investigation of cell type conservation reveals a shared gene signature between glial cells of mouse, fly and octopus. Genes related to learning and memory are enriched in vertical lobe cells, which show molecular similarities with Kenyon cells in Drosophila. We construct a cell type taxonomy revealing transcriptionally related cell types, which tend to appear in the same brain region. Together, our data sheds light on cell type diversity and evolution in the octopus brain.
| S-EPMC9712504 | biostudies-literature
Project description:Coleoid cephalopods possess a highly complex nervous system and a rich behavioral repertoire that is unique within the invertebrates and is comparable to – but evolved independently from – the vertebrates (Shigeno et al. 2018). To explain this complexity, previous studies have implicated a unusually high level of mRNA editing in transcripts expressed in both the octopus and squid nervous system (Albertin et al. 2015; Alon et al. 2015; Liscovitch-Brauer et al. 2017). We have sequenced RNA across 18 tissues from the octopus O. vulgaris, and analyzed the extent of mRNA isoform usage as well as the expression of microRNAs in the nervous system in comparison to non-neuronal tissues.
2022-11-11 | GSE192550 | GEO
Project description:To understand the complexity of the brain, connectome and transcriptome maps of high resolution are being generated, but an equivalent catalogue of the brain proteome is lacking. To provide a starting point, we have performed an in-depth proteome analysis of the adult mouse brain, its major regions and cell types, which resulted in the so far largest collection of cell-type resolved protein expression data of the brain. Comparisons of the 12,934 identified proteins in oligodendrocytes, astrocytes, microglia and cortical neurons with deep sequencing data of the transcriptome indicated deep coverage of the proteome. We identified novel protein makers for different cell type and brain regions. These were validated either directly such as in case of cell types or by comparative analysis against Allen mouse brain atlas. The utility and the power of the resource were demonstrated by the identification of Lsamp, an adhesion molecule of the IgLON family, as a negative regulator of myelination in a subpopulation of neurons. Our in-depth proteome analysis of CNS cell types provides a framework towards a system-level understanding of cell type diversity in the CNS and serves as a rich resource to the neuroscience community for the better understanding of brain development and function.
2015-10-29 | PXD001250 | Pride
Project description:To understand the complexity of the brain, connectome and transcriptome maps of high resolution are being generated, but an equivalent catalogue of the brain proteome is lacking. To provide a starting point, we have performed an in-depth proteome analysis of the adult mouse brain, its major regions and cell types, which resulted in the so far largest collection of cell-type resolved protein expression data of the brain. Comparisons of the 12,934 identified proteins in oligodendrocytes, astrocytes, microglia and cortical neurons with deep sequencing data of the transcriptome indicated deep coverage of the proteome. We identified novel protein makers for different cell type and brain regions. These were validated either directly such as in case of cell types or by comparative analysis against Allen mouse brain atlas. The utility and the power of the resource were demonstrated by the identification of Lsamp, an adhesion molecule of the IgLON family, as a negative regulator of myelination in a subpopulation of neurons. Our in-depth proteome analysis of CNS cell types provides a framework towards a system-level understanding of cell type diversity in the CNS and serves as a rich resource to the neuroscience community for the better understanding of brain development and function.
2020-02-08 | MSV000084941 | MassIVE
Project description:We performed paired end Illumina Hiseq on bulk tissues of Octopus bimaculoides sensory tissues, Libaries were sequenced on two different Lanes
2020-08-25 | GSE156748 | GEO
Project description:Three adult individuals of the Octopus vulgaris were collected from the Southern Tyrrhenian Sea (Italy). For each animal, total RNA was isolated from the supra- (SEM), sub- (SUB) esophageal masses, optic lobes (OL) and the arms (ARM). The RNA-sequencing has been performed using Illumina technology.
2022-04-15 | E-MTAB-3957 | biostudies-arrayexpress
Project description:This study was carried out to investigate the gene expression profile from arm and hatchlings transcriptome across multiple individual Octopus bimaculoides .
2022-06-30 | GSE188925 | GEO
Project description:Neuronal diversity is a defining feature of the mammalian brain deemed necessary for realizing the complex function of the nervous system. In order to begin to understand the transcriptional basis of this diversity, we collected more than 170 neuronal and non-neuronal cell type-specific transcriptomes defined operationally by transgenic mouse lines and anatomical regions. The dataset indicates that the genes specifically expressed in neuronal cell types are biased toward long genes. We revealed that these long genes have higher capacities to be differentially expressed between cell types and thus assume an important role in diversification of the neuronal transcriptomes. Since mobile element insertions are the main cause of the gene elongations, we propose that exaptation of the inserted mobile elements significantly contributed to the neuronal diversity.
2018-07-20 | GSE79238 | GEO