Single-cell RNA-sequencing of Platynereis dumerilii larval brain cells
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REPOSITORIES: ENA
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Project description:Understanding cell type identity in complex tissues or organisms requires integration of each cell's expression profile with its spatial location within the tissue under study. We developed a high-throughput method that combines in vitro single-cell RNA-sequencing with a gene expression atlas to map single cells back to their location within the tissue of interest. We used the developing brain of a marine annelid, Platynereis dumerilii that is an important model system for studying bilaterian brain evolution, to benchmark our approach. To generate the single-cell mRNA-sequencing data, P. dumerilii larval brains were dissociated, followed by cell capture, cDNA synthesis and amplification on the C1 Single-Cell Auto Prep IFC for 10-17 um cells (Fluidigm). Sequencing libraries were produced using Nexera XT DNA kit (Illumina). In total, we sequenced 213 samples, of which 129 correspond to single, alive cells (as judged by visual inspection of the captured cells) with the remainder consisting of a variety of single dead cells (n=18), wells containing extracellular matrix contaminants (n=8) or multiple cells (n=17), as well as a negative controls where no cells were observed (n=41). For this dataset, we achieved ~90% success rate for the spatial mapping of the single-cell RNA-seq data to P. dumerilii brain atlas. NOTE: 72 additional samples were added on 13th December 2014.
2014-12-13 | E-MTAB-2865 | biostudies-arrayexpress
Project description:For unbiased, whole-organism wide cell type profiling, we randomly sampled cells from dissociated Platynereis larvae. To generate the single-cell mRNA-sequencing data, P. dumerilii larvae were dissociated, followed by cell capture, cDNA synthesis and amplification on the C1 Single-Cell Auto Prep IFCs for 5-10 um or 10-17 um cells (Fluidigm). Sequencing libraries were produced using Nexera XT DNA kit (Illumina). In total, we sequenced 596 samples, of which 373 correspond to single, alive cells that passed the quality check criteria. Part of this dataset was previously published (ArrayExpress accession number E-MTAB-2865). Here, we publish additional 383 sequenced cells.
2017-09-18 | E-MTAB-5953 | biostudies-arrayexpress
Project description:Single-cell RNA-sequencing of Platynereis dumerilii
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Project description:Platynereis dumerilii high resolution developmental transcriptomic time-course
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Project description:Single cell transcriptome atlas of the Drosophila larval brain
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Project description:The cellular composition of the brain and how it is affected by starvation, remains largely unknown. Here we introduce a single-cell transcriptome atlas of the entire Drosophila melanogaster first instar larval brain. We first assigned cell type identity based on the expression of previously characterized marker genes, allowing us to distinguish five major groups: neural progenitors cells, differentiated neurons, glial cells, undifferentiated neurons as well as non-neural cells corresponding to organs and structures located adjacent to the brain. All major classes were further subdivided into multiple subtypes based on cluster analysis, revealing critical biological features of various cell types. Moreover, we included two different feeding conditions: normal fed versus starved. After starvation, the transcriptional profile of several cell clusters were altered, while the overall composition of the brain remains unaffected. Intriguingly, different cell clusters show very distinct responses to starvation, suggesting the presence of cell-specific programs for nutrition availability. Establishing a single-cell transcriptome atlas of the larval brain provides a powerful tool to explore cell diversity, assess genetic profiles of neurogenic, neuronal and glial cell types. The analysis of neurotransmitters, neuropeptides and their respective receptors may further open the doors for functional studies.
2019-11-15 | GSE134722 | GEO
Project description: Not available
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