Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Seawater metagenome

ABSTRACT: Amplicon sequencing of 18S rRNA gene, eukaryote assemblages in seawater in Matsushima Bay, Japan

PROVIDER: PRJDB13931 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR398897_1.fastq.gz	Fastqsanger.gz
	DRR398897_2.fastq.gz	Fastqsanger.gz
	DRR398898_1.fastq.gz	Fastqsanger.gz
	DRR398898_2.fastq.gz	Fastqsanger.gz
	DRR398899_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 1764

Similar Datasets

18s rRNA gene in seawater and sea ice of Aoshan bay

Project description:18s rRNA gene in seawater and sea ice of Aoshan bay

| PRJNA908654 | ENA

Synthetic contaminants discovered from biomass filtered seawater and extracted shellfish meat

Project description:Untargeted LC-MS/MS files of biomass filtered seawater and extracted shellfish meat from Narragansett Bay, RI.

2024-12-27 | MSV000096738 | MassIVE

18s rRNA gene in seawater and sea ice of Aoshan bay

Project description:18s rRNA gene in seawater and sea ice of Aoshan bay Raw sequence reads

| PRJNA908643 | ENA

The integrated stress response regulates 18S nonfunctional rRNA decay in mammals

Project description:Abstract - 18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.

2024-12-09 | MSV000096620 | MassIVE

Lake George 2009 water sampling

Project description:18S rRNA amplicon sequencing of eukaryote communities in Lake George, ND, USA

| PRJEB33421 | ENA

Lake George 2009 water sampling

Project description:18S rRNA amplicon sequencing of eukaryote communities in Lake George, ND, USA

| PRJEB33420 | ENA

metagenome

Project description:Amplicon sequencing of 16S rRNA and PsbA gene, prokaryote and phytoplankton assemblages in sediments and seawater near Nagatsura-Ura Lagoon, Japan

| PRJDB12008 | ENA

seawater

Project description:Seawater 16S amplicon sequencing

| PRJNA577349 | ENA

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (RNA-Seq)

Project description:Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S rRNA 3’ end maturation during late-40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the effects of eIF5B have not been studied at the genome-wide level in any organism, and 18S rRNA 3’ end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat-stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3’ end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3’ end maturation or metabolism. We quantitatively defined new processing hotspots and identified adenylation as the prevalent non-templated RNA modification at the 3’ ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNAi to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3’ portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late-40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, mRNA translation initiation, and siRNA biogenesis in plants.

2023-04-19 | GSE223169 | GEO

Arabidopsis HOT3/eIF5B1 constrains rRNA RNAi by facilitating 18S rRNA maturation during translation initiation (Ribo-Seq)

2023-04-19 | GSE223168 | GEO