Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Marine plankton metagenome

ABSTRACT: Plankton biodiversity monitoring by environmental DNA: a multiple marker study

PROVIDER: PRJDB12325 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR320834_1.fastq.gz	Fastqsanger.gz
	DRR320834_2.fastq.gz	Fastqsanger.gz
	DRR320835_1.fastq.gz	Fastqsanger.gz
	DRR320835_2.fastq.gz	Fastqsanger.gz
	DRR320836_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 384

Similar Datasets

Single-organism multimodal characterisation of eukaryotic plankton with Ukiyo-e-Seq

Project description:We used single-cell sequencing data and imaging to investigate Eukaryotic plankton from environmental marine samples collected from Coogee, NSW, Australia.

2024-08-18 | GSE274796 | GEO

marine plankton metagenome

Project description:marine plankton metagenome Targeted loci environmental

| PRJNA387546 | ENA

marine plankton environmental sample

Project description:marine plankton environmental sample overview

| PRJNA642200 | ENA

High-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton

Project description:In this study we applied MASC-seq (massive and parallel microarray sequencing, https://doi.org/10.1038/ncomms13182), a scRNA-seq method that facilitates sequencing of thousands of cells in parallel, and that couples microscope images with the single cell transcriptome data. For this method, fixed cells are spread over a microarray with 100 μm-sized spots of DNA capture probes with spot-specific indices. The cells are first imaged using a scanning microscope and then permeabilized, releasing their RNA out of the cells and bind to the probes on the array. cDNA is synthesized, harvested and sequenced, and, using the spot-specific barcode-sequences, cDNA sequences stemming from a specific spot (i.e., cell) can be linked to the microscope image of the corresponding cell. However, until now, the MASC-seq method has only been applied to mammalian cells. The aim of this study was to test and adapt the MASC-seq method for application on unicellular eukaryotic plankton. We applied and optimized the method on three cultured plankton representatives, abundant in communities of aquatic environments, Phaeodactylum tricornutum (a diatom, silica and polysaccharide cell walls 23), Heterocapsa sp. (a dinoflagellate, cellulose thecal plates 24) and Tetrahymena thermophila (a ciliate, lipid membrane 25) which all have different size and diverse cell surface structures common to plankton. We optimized several steps in the protocol to make it more suitable for planktonic cells and compared the results from MASC-seq generated single cell transcriptomes to bulk RNA sequencing.

2022-10-26 | E-MTAB-12261 | biostudies-arrayexpress