Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pseudouridine modification detection in mRNA

ABSTRACT: Pseudouridine modification detection in mRNA

PROVIDER: PRJEB56934 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina)

Project description:Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.

2021-11-18 | GSE180655 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

2021-11-18 | GSE180654 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

Project description:Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

| PRJNA749031 | ENA

Pseudouridine in small RNAs

Project description:Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis.

2023-08-07 | GSE230228 | GEO

A radiolabeling-free, qPCR-based method for locus-specific pseudouridine detection

Project description:Pseudouridine (Ψ) is the most abundant post-transcriptional RNA modification. Various methods have been developed to achieve locus-specific Ψ detection; however, the existing methods often involve radiolabeling of RNA, require advanced experimental skills and can be time-consuming. Herein we report a radiolabeling-free，qPCR-based method to detect locus-specific Ψs in rRNA and mRNA. This method is based on Ψ chemical adduct (Ψ-CMC) induced mutation/deletion during reverse transcription (RT), leading to qPCR products of different melting temperatures. Utilizing high-throughput sequencing, we demonstrate that such misincorporation is a general feature of Ψ-CMC adduct during our improved RT conditions. We validated this method on known Ψ sites in rRNA and showed that the melting curves correlate with the modification level. Moreover, we successfully detected Ψs in mRNA and lncRNA of different abundance, and identified Ψ synthase that targets mRNA. Our facile method takes only 1.5 days to complete, and with slight adjustment it can be applied to detect other epitranscriptomic marks in the transcriptome.

2017-10-03 | GSE102476 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina)

Project description:Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina)

| PRJNA749033 | ENA

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

Project description:Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

| PRJNA749032 | ENA

Project description:Pseudouridine modification detection in mRNA

| PRJNA777450 | ENA

Bisulfite Incorporation Hindered Ligation-based Method for Locus-Specific Detection and Quantification of Pseudouridine

Project description:We applied BIHIND-seq to 15 sites of Hela 18S rRNA to probe Pseudouridine modification at the target sites and checked how pseudouridine level changed after DKC1 knockdown.

2024-11-01 | GSE269170 | GEO

Pseudouridine in small RNAs

2023-08-07 | GSE222751 | GEO