Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

ABSTRACT: Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

PROVIDER: PRJNA229098 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1032110.fastq.gz	Fastqsanger.gz
	SRR1032120.fastq.gz	Fastqsanger.gz
	SRR1032130.fastq.gz	Fastqsanger.gz
	SRR1032140.fastq.gz	Fastqsanger.gz
	SRR1032111.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 37

Similar Datasets

Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

Project description:We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

2014-02-07 | GSE52489 | GEO

Ribonuclease L and Metal-Ion-Independent Endoribonuclease Cleavage Sites in Host and Viral RNAs

Project description:We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. To make cDNA libraries, we exploited the 2’, 3’-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion-independent endoribonucleases. Using Arabidopsis thaliana tRNA ligase, RNA fragments with 2’, 3’-cyclic phosphates were covalently attached to defined RNA linkers containing an 8-base long unique molecular identifier (UMI) sequence. Libraries prepared in this manner contain cDNA derived exclusively from RNA fragments with 2', 3'-cyclic phosphates. The UMI sequence allows for detailed quantitation. We optimized and validated 2’, 3’-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A, and RNA from uninfected and poliovirus-infected HeLa cells.

2014-02-07 | E-GEOD-52489 | biostudies-arrayexpress

Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs.

Project description:Ribonuclease L (RNase L) is a metal-ion-independent endoribonuclease associated with antiviral and antibacterial defense, cancer and lifespan. Despite the biological significance of RNase L, the RNAs cleaved by this enzyme are poorly defined. In this study, we used deep sequencing methods to reveal the frequency and location of RNase L cleavage sites within host and viral RNAs. To make cDNA libraries, we exploited the 2', 3'-cyclic phosphate at the end of RNA fragments produced by RNase L and other metal-ion-independent endoribonucleases. We optimized and validated 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing methods using viral RNAs cleaved with purified RNase L, viral RNAs cleaved with purified RNase A and RNA from uninfected and poliovirus-infected HeLa cells. Using these methods, we identified (i) discrete regions of hepatitis C virus and poliovirus RNA genomes that were profoundly susceptible to RNase L and other single-strand specific endoribonucleases, (ii) RNase L-dependent and RNase L-independent cleavage sites within ribosomal RNAs (rRNAs) and (iii) 2', 3'-cyclic phosphates at the ends of 5S rRNA and U6 snRNA. Monitoring the frequency and location of metal-ion-independent endoribonuclease cleavage sites within host and viral RNAs reveals, in part, how these enzymes contribute to health and disease.

| S-EPMC4005677 | biostudies-literature

Endoribonuclease activity in hepatitis C virus-infected Huh7.5.1 cells

Project description:We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and endoribonuclease cleavage sites in host and viral RNAs during HCV infection of Huh7.5.1 cells

2022-08-06 | GSE72144 | GEO

Ribonuclease L Targets Discrete Sites in Influenza Virus RNA

Project description:We used 2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing to identify and quantify ribonuclease L cleavage sites in host and viral RNAs.

2014-12-16 | GSE60581 | GEO

metal stress 2

Project description:Effect of mild metal ion - stress (500µM AlCl3, 500µM VCl3, 1.5mM ZnCl2) on cellular metabolism, resp. on transcription - 30min incubation in yeast Saccharomyces cerevisiae (JSwt - is a FY derivate; MATaleu2ura3trp1HIS3)

2011-05-01 | E-MEXP-2987 | biostudies-arrayexpress

metal stress 1

Project description:Effect of mild metal ion-stress (40µM AgNO3, 200µM AsCl3, 2µM CdCl2, 100µM CoCl2, 30µM HgCl2, 1.5mM MnCl2, 1.5mM NiSO4) on cellular metabolism, resp. on transcription - 30min incubation in yeast Saccharomyces cerevisiae

2011-01-01 | E-MEXP-2985 | biostudies-arrayexpress

A novel peptide hydrogel of metal ion clusters for accelerating bone defect regeneration

Project description:A novel peptide hydrogel of metal ion clusters for accelerating bone defect regeneration

| PRJNA874756 | ENA

Queuosine modification protects cognate tRNAs against ribonuclease cleavage

Project description:Eukaryotic transfer RNAs (tRNA) contain on average 13 modifications that perform a wide range of roles in translation and in the generation of tRNA fragments that regulate gene expression. Queuosine (Q) modification occurs in the wobble anticodon position of tRNAs for amino acids His, Asn, Tyr, and Asp. In eukaryotes, Q modification is fully dependent on diet or on gut microbiome in multi-cellular organisms. Despite decades of study, cellular roles of Q modification remain to be fully elucidated. Here we show that in human cells, Q modification specifically protects its cognate tRNAHis and tRNAAsn against cleavage by ribonucleases. We generated cell lines that contain completely depleted or fully Q-modified tRNAs. Using these resources, we found that Q modification significantly reduces angiogenin cleavage of its cognate tRNAs in vitro. Q modification does not change the cellular abundance of the cognate full-length tRNAs, but alters the cellular content of their fragments in vivo in the absence and presence of stress. Our results provide a new biological aspect of Q modification and a mechanism of how Q modification alters small RNA pool in human cells.

2018-08-10 | GSE102570 | GEO

A novel peptide hydrogel of metal ion clusters for accelerating bone defect regeneration

Project description:We explore the genes and pathways related to metal ions involved in extracellular matrix, cell adhension and migration, expression of cytokine, antibacterial, inflammation, and cell signaling.

2022-09-01 | GSE212279 | GEO

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