Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA-sequencing of Platynereis dumerilii larval brain cells

ABSTRACT: Single-cell RNA-sequencing of Platynereis dumerilii larval brain cells

PROVIDER: PRJEB7134 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR592498_1.fastq.gz	Fastqsanger.gz
	ERR592498_2.fastq.gz	Fastqsanger.gz
	ERR592499_1.fastq.gz	Fastqsanger.gz
	ERR592499_2.fastq.gz	Fastqsanger.gz
	ERR592500_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 570

Similar Datasets

Single-cell RNA-sequencing of Platynereis dumerilii larval brain cells

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

Platynereis dumerilii

Project description:Platynereis dumerilii

| PRJNA37751 | ENA

Platynereis dumerilii

Project description:Platynereis dumerilii Transcriptome

| PRJNA271451 | ENA

Single-cell RNA-sequencing of Platynereis dumerilii

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

Platynereis dumerilii

Project description:Platynereis dumerilii Genome sequencing and assembly

| PRJNA893673 | ENA

Platynereis dumerilii

Project description:Platynereis dumerilii high resolution developmental transcriptomic time-course

| PRJNA272544 | ENA

Single-cell RNA-sequencing of Platynereis dumerilii

Project description:Single-cell RNA-sequencing of Platynereis dumerilii

| PRJEB22558 | ENA

Platynereis posterior regeneration transcriptome

Project description:Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii