Platynereis head transcriptome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB27496 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A maturation, sex and lunar phase locked Platynereis head proteome was generated by sampling six heads per biological replicate from male and female Platynereis at defined stages of sexual maturation (immature, premature and mature) at two different moon phases; New moon and Free-running Full moon, meaning the animals would expect a nocturnal light stimulus, Full moon, which was not given. From these heads RNA and protein were extracted simultaneously and used for both transcriptomics (ENA accession no. PRJEB27496) and quantitative proteomics. In total 2290 proteins were identified with two unique peptides as requirement; of these, 1064 proteins were found to be quantifiable (identification in two out of three biological replicates and three out of five technical replicates). Relative quantification revealed that the majority of quantifiable proteins changed during maturation (693 out of 1064 proteins), sexual differences accounted for only 17 differentially expressed proteins, whereas lunar phase differences showed 261 differentially expressed proteins. This finding is in contrast to what was found on the transcriptome levels where differences in between the lunar phases only accounted for only 64 out of 52059 transcripts. To confirm this high degree of lunar regulated proteins a second proteome from immature animals at New moon and Free-running Full moon was undertaken. In this second set, we identified 2095 proteins of which 1671 were considered quantifiable. Of these 173 proteins showed significant differences between the New moon and the Free running full moon phase, thus confirming the previous results of a higher regulation on the protein compared to the transcript levels.
2019-02-19 | PXD010532 | Pride
Project description:Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii
| PRJEB60036 | ENA
Project description:Platynereis dumerilii Genome sequencing and assembly
| PRJNA893673 | ENA
Project description:Platynereis dumerilii high resolution developmental transcriptomic time-course
| PRJNA272544 | ENA
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
| PRJEB22558 | ENA
Project description:The extent to which plants can enhance human life support on other worlds depends on the ability of plants to thrive in extraterrestrial environments using in situ resources. Using samples from Apollo 11, 12 and 17, we show that the terrestrial plant Arabidopsis thaliana germinates and grows in diverse lunar regoliths. However, our results show that growth is challenging; the lunar regolith plants were slow to develop, expressed genes indicative of ionic stresses, and many showed severe stress morphologies. Therefore, although in situ lunar regolith can be useful for plant production in lunar habitats, they are not benign substrates. The interaction between plants and lunar regolith will need to be further elucidated, and likely mitigated, to enable efficient use of lunar regolith for life support.
2022-05-16 | GSE188852 | GEO
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