Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantification of induced RNA mutation by nucleoside analogs in the repRNA-v4 EGFP region

ABSTRACT: Quantification of induced RNA mutation by nucleoside analogs in the repRNA-v4 EGFP region

PROVIDER: PRJNA1133798 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Quantification of induced RNA mutation by nucleoside analogs in the repRNA-v4 EGFP region

Project description:REPLACE was engineered from an orthogonal alphaviral RNA replication system. It generates a large, continuously diversified library of replicative RNAs through a replicase-limited mode of replication and inducible mutagenesis. We analyzed the variation of RNA mutations induced by two nucleoside analogues over time and at different concentrations. This data was used to guide the construction of RNA mutant libraries.

2024-09-30 | GSE271881 | GEO

Quantification of basal RNA mutation rate in the repRNA-v4 EGFP region

Project description:Quantification of basal RNA mutation rate in the repRNA-v4 EGFP region

| PRJNA1133799 | ENA

The search for enzymes responsible for metabolism of nucleoside analogs

Project description:Affymetrix U95Av2 expression data from human intestinal cells (Caco-2) and tissues from all intestinal segments (duodenum, jejunum, ileum, colon). Entries contain the search terms "glycosylase, phosphorylase, cytochrome or nucleoside," which were relevant to our search for enzymes capable of cleaving the N-glycosidic bond of nucleoside analog drugs. Keywords = glycosylase Keywords = phosphorylase Keywords = nucleoside Keywords: parallel sample

2005-10-30 | GSE1862 | GEO

Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance [Array]

Project description:We show that high DCTPP1 expression was associated with cell-intrinsic resistance to nucleoside DNMT inhibition, and that triptolide and its analogs could overcome this resistance.

2024-10-01 | GSE185594 | GEO

Triptolide sensitizes cancer cells to nucleoside DNA methyltransferase inhibitors through inhibition of DCTPP1 mediated cell-intrinsic resistance [RNA-Seq]

2024-10-01 | GSE185650 | GEO

Nucleos(t)ide analogs for hepatitis B virus infection differentially regulate the growth factor signaling in hepatocytes

Project description:Recent clinical studies have suggested that the risk of developing hepatocellular carcinoma might be lower in chronic hepatitis B (CHB) patients receiving tenofovir disoproxil fumarate (TDF) than in patients receiving entecavir (ETV), although there is no difference in biochemical and virological remission between two drugs. The effects of nucleoside analogs (NsAs; lamivudine and ETV) or nucleotide analogs (NtAs; adefovir disoproxil [ADV], TDF, and tenofovir alafenamide [TAF]) on cell growth and the expression of growth signaling molecules were investigated. The tumor inhibitory effects of NsAs or NtAs were evaluated using a mouse xenograft model, and protein phosphorylation profiles were investigated.

2024-01-17 | GSE249861 | GEO

Quantification of basal RNA mutation rate in the repRNA-v4 EGFP region

Project description:REPLACE was engineered from an orthogonal alphaviral RNA replication system. It generates a large, continuously diversified library of replicative RNAs through a replicase-limited mode of replication and inducible mutagenesis. We analyzed the mutation frequency at Day0 (IVT RNA), Day1, Day3, Day7, Day14, Day21 and DNA plasmid to estimate the RNA mutation rate. This data was used to guide the construction of RNA mutant libraries.

2024-09-30 | GSE271880 | GEO

Sphingobium sp. V4 strain:V4

Project description:Sphingobium sp. V4 strain:V4 Genome sequencing

| PRJNA753255 | ENA

Immunoprecipitated proteins associated with foci-forming Eno2p-EGFP-FLAG or non-forming Eno2V22Ap-EGFP-FLAG in yeast Saccharomyces cerevisiae under hypoxia

Project description:Yeast enolase (Eno2p) conjugated with EGFP and Flag-tag (Eno2p-EGFP-FLAG) and Eno2p with V22A substitution (Eno2V22Ap) conjugated with EGFP and Flag-tag (Eno2V22Ap-EGFP-FLAG) were produced in baker's yeast S. cerevisiae. After semi-anaerobic culture at 30 ˚C for 12h, cells producing Eno2p-EGFP-FLAG formed fluorescent foci, while cells producing Eno2V22Ap-EGFP-FLAG did not. The cells were collected and lysed, and proteins Eno2p-EGFP-FLAG or Eno2V22Ap-EGFP-FLAG and the associated proteins were coimmunoprecipitated using ANTI-FLAG M2 affinity gel and analyzed. Data contain two biological replicates and two technical replicates (n = 4). As the results, 96 proteins were detected with both recombinant Eno2p-EGFP-FLAG and Eno2V22Ap-EGFP-FLAG protein, 29 proteins were detected only with recombinant Eno2p-EGFP-FLAG protein, and 16 proteins were detected only with recombinant Eno2V22Ap-EGFP-FLAG protein. Data Processing/Data Analysis: The separated analytes were detected on an LTQ Velos linear ion trap mass spectrometer (Thermo Scientific). For data-dependent acquisition, the method was set to automatically analyze the five most intense ions observed in the MS scan. The mass spectrometry data were used for protein identification by the Mascot search engine on Protein Discoverer software (ver. 1.2, Thermo Scientific) against the information in the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org). Search parameters for peptide identification included a precursor mass tolerance of 1.2 Da, a fragment mass tolerance of 0.8 Da, a minimum of one tryptic terminus, and a maximum of one internal trypsin cleavage site. Cysteine carbamidomethylation (+57.021 Da) and methionine oxidation (+15.995 Da) were set as a differential amino acid modification. The data were then filtered at a q value ≤ 0.01 corresponding to 1% FDR at the spectral level.

2014-02-25 | PXD000173 | Pride

Activation of SIRT6 by DNA hypomethylating agents and clinical consequences on combination therapy in leukemia

Project description:The FDA-approved DNA hypomethylating agents (DHAs) like 5-azacytidine (5AC) and decitabine (DAC) demonstrate efficacy in the treatment of hematologic malignancies. Despite previous reports that showed histone acetylation changes upon using these agents, the exact mechanism underpinning these changes is unknown. In this study, we investigated the relative potency of the nucleoside analogs and non-nucleoside analogs DHAs on DNA methylation reversal using DNA pyrosequencing. Additionally, we screened their effect on the enzymatic activity of the histone deacetylase sirtuin family (SIRT1, SIRT2, SIRT3, SIRT5 and SIRT6) using both recombinant enzymes and nuclear lysates from leukemia cells. The nucleoside analogs (DAC, 5AC and zebularine) were the most potent DHAs and increased the enzymatic activity of SIRT6 without showing any significant increase in other sirtuin isoforms. ChIP-Seq analysis of bone marrow cells derived from six acute myeloid leukemia (AML) patients and treated with the nucleoside analog DAC induced genome-wide acetylation changes in H3K9, the physiological substrate for SIRT6. Data pooling from the six patients showed significant acetylation changes in 187 gene loci at different chromosomal regions including promoters, coding exons, introns and distal intergenic regions. Signaling pathway analysis showed that H3K9 acetylation changes are linked to AML-relevant signaling pathways like EGF/EGFR and Wnt/Hedgehog/Notch. To our knowledge, this is the first report to identify the nucleoside analogs DHAs as activators of SIRT6. Our findings provide a rationale against the combination of the nucleoside analogs DHAs with SIRT6 inhibitors or chemotherapeutic agents in AML due to the role of SIRT6 in maintaining genome integrity and DNA repair.

2020-07-28 | GSE152804 | 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