Platynereis dumerilii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271451 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1743016.fastq.gz | Fastqsanger.gz | |||
| SRR1742987_1.fastq.gz | Fastqsanger.gz | |||
| SRR1742987_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Platynereis dumerilii Genome sequencing and assembly
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Project description:Platynereis dumerilii high resolution developmental transcriptomic time-course
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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: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:Single-cell RNA-sequencing of Platynereis dumerilii larval brain cells
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Project description:Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii
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Project description:Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a ‘zootypic’ stage, however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum, including a segmented worm, a flatworm, a roundworm, a water bear, a fruitfly, a sea urchin, a zebrafish, a sea anemone, a sponge, and a comb jelly. For each species, we collected the embryonic transcriptomes at ~100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly, we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation, and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes, also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility.
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