Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Genome-wide sequencing uncovers cryptic diversity and mito-nuclear discordance in the Octopus vulgaris species complex.

PROVIDER: PRJNA679979 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13153210_1.fastq.gz	Fastqsanger.gz
	SRR13153210_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Thymelicus sylvestris

Project description:A mirage of cryptic species: genomics uncover striking mito-nuclear discordance in the skipper butterfly Thymelicus sylvestris

| PRJNA531653 | ENA

Project description:Central Texas Eurycea extreme mito-nuclear discordance

| PRJNA655735 | ENA

Mapping and understanding the function of RNA in octopus brain

Project description:Coleoid cephalopods possess a highly complex nervous system and a rich behavioral repertoire that is unique within the invertebrates and is comparable to – but evolved independently from – the vertebrates (Shigeno et al. 2018). To explain this complexity, previous studies have implicated a unusually high level of mRNA editing in transcripts expressed in both the octopus and squid nervous system (Albertin et al. 2015; Alon et al. 2015; Liscovitch-Brauer et al. 2017). We have sequenced RNA across 18 tissues from the octopus O. vulgaris, and analyzed the extent of mRNA isoform usage as well as the expression of microRNAs in the nervous system in comparison to non-neuronal tissues.

2022-11-11 | GSE192550 | GEO

RNA-seq of the Octopus vulgaris nervous system.

Project description:Three adult individuals of the Octopus vulgaris were collected from the Southern Tyrrhenian Sea (Italy). For each animal, total RNA was isolated from the supra- (SEM), sub- (SUB) esophageal masses, optic lobes (OL) and the arms (ARM). The RNA-sequencing has been performed using Illumina technology.

2022-04-15 | E-MTAB-3957 | biostudies-arrayexpress

Identifying natural bioactive peptides from the ink by-product of common octopus (Octopus vulgaris) using proteomics

Project description:Identifying natural bioactive peptides from the ink by-product of common octopus (Octopus vulgaris) using proteomics

2022-07-15 | MSV000089896 | MassIVE

Identifying natural bioactive peptides from the common octopus (Octopus vulgaris Cuvier, 1797) skin mucus by-products using proteogenomic analysis

Project description:Identifying natural bioactive peptides from the common octopus (Octopus vulgaris Cuvier, 1797) skin mucus by-products using proteogenomic analysis

2022-07-14 | MSV000089888 | MassIVE

Cell type diversity in the octopus brain

Project description:Octopuses are mollusks that evolved intricate neural systems which are comparable with vertebrates in terms of cell number, complexity and size. Exactly how an octopus increases its neural cell number so dramatically and whether an increase in cell type diversity enables higher cognitive function and complex behavior is still unknown. To profile the cell diversity of the developing octopus brain we applied 10x Genomics’ single-cell/nuclei RNA sequencing technology. At hatching, the Octopus vulgaris brain possesses the main lobes and connections of an adult brain, but which cell types are present remains elusive. We were able to identify 42 robust cell types comprising mostly neural cells, as well as multiple glial subtypes and other non-neuronal populations such as endothelial cells and fibroblasts. In situ expression analysis of marker genes allowed spatial mapping of clusters, including vertical lobe cells and several optic lobe cell types. Investigation of cell type conservation indicated similar gene expression signatures between glial cells of mice, fly and octopus. Genes related to memory and learning were found enriched in vertical lobe cells, that showed molecular similarities with Kenyon cells in Drosophila but not to any mouse cell type. Lastly, we also analyzed the expression of newly expanded gene families (protocadherins, C2H2 zinc-finger transcription factors and G-protein coupled receptors) and found that these are enriched in specific cell types. Taken together, our data gives insight into cell type evolution and the composition of the complex octopus brain.

2022-01-31 | GSE193622 | GEO

Shotgun proteomics analysis of saliva and salivary gland tissue from the common octopus Octopus vulgaris

Project description:The saliva of the common octopus (Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioural studies and molecular analysis on O. vulgaris and related species suggests that it should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the salivary gland transcriptome of O. vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.

2018-09-24 | PXD010298 | Pride

Decoding Octopus Mucus: Impact of Aquarium-Maintenance and Senescence on the Skin Mucus Proteome Profile of the Common Octopus (Octopus vulgaris)

Project description:This work investigates the comparison of protein profiles in the Octopus vulgaris skin mucus of wild, aquarium-maintained, and senescent specimens to identify potential welfare biomarkers, using tandem mass tag (TMT) in an Orbitrap Eclipse Tribrid mass spectrometer to create a reference dataset from octopus skin mucus obtained in different conditions.

2025-05-07 | PXD052915 | Pride

The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [expression array]

Project description:Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts. Genome-wide expression analysis of MTREC, Nuclear Exosome, TRAMP, Nrd complex members All experiments were performed twice in biological replicates, except that rmn1Δ and mmi1Δ mei4-P572 were perfomed once.

2015-05-22 | E-GEOD-64979 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data