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

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

PROVIDER: PRJNA1120450 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29297792.fastq.gz	Fastqsanger.gz
	SRR29297793.fastq.gz	Fastqsanger.gz
	SRR29297794.fastq.gz	Fastqsanger.gz
	SRR29297795.fastq.gz	Fastqsanger.gz
	SRR29297796.fastq.gz	Fastqsanger.gz

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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

Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

Project description:Hairpin-containing pre-miRNAs are precursors of microRNAs (miRNAs) that play important roles in cellular processes and various human diseases. Pre-miRNAs are produced from longer primary transcripts (pri-miRNAs). The falsity in cellular expression and sequences of pre-miRNAs might cause cellular defects or human diseases. However, the current pre-miRNA quantification methods by qPCR cannot discriminate between pre-miRNAs and their parental pri-miRNAs. In addition, the ligation of the sequencing adapter to 5’-end of pre-miRNAs is inefficient, therefore, pre-miRNA sequencing is highly impractical. Here, we developed a method, called the intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing. This method utilized T4 RNA ligase 1 to convert hairpin-pre-miRNAs into circularized RNAs that do not naturally exist in cells. The resulting circuliarized RNAs allow us to design unique primers to quantify pre-miRNAs by qPCR specicially, and thus this qPCR can distinguish pre-miRNA from pri-miRNAs. In addition, the iLIME also allows us to sequence pre-miRNAs using next-generation sequencing. The iLIME method offers a simple and effective way to quantify and sequence pre-miRNAs. This will be useful in investigating pre-miRNAs for addressing research questions for medical applications. The iLIME can be potentially extended to other hairpin-containing RNAs, such as tRNAs and snRNAs.

2021-10-11 | GSE185524 | GEO

Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

Project description:Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

| PRJNA769430 | 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 | GSE222751 | GEO

Pseudouridine in small RNAs

2023-08-07 | GSE230228 | GEO

Knockout of Pseudouridine synthase 1 (PUS1) in mice. [Kidney]

Project description:In an effort to produce a mouse model of Mitochondrial Myopathy with Lactic acidosis and Sideroblastic Anemia (MLASA), we knocked out the gene for Pseudouridine synthase 1 (PUS1), an enzyme that modifies uridine to pseudouridine in many cytoplasmic and mitochondrial tRNAs, as well as other cellular RNAs. The Pus1-/- mice are viable, are born at the expected Mendelian frequency, and are non-dysmorphic. The PUS1 mRNA and certain pseudouridine modifications are absent in cytoplasmic and mitochondrial tRNAs in the Pus1-/- mice. The Pus1-/- mice display reduce exercise capacity at 14 weeks, with alterations in muscle morphology, histology, and physiology. Red gastrocnemius muscle from Pus1-/- mice shows reduced number and size of mitochondria and reduced Cytochrome C oxidase activity. Two-condition, two-color experiment: Mouse wild type PUS1 and homozygous mutant PUS1 kidney tissue samples: 4 biological replicates each.

2016-05-16 | E-GEOD-77819 | biostudies-arrayexpress

Knockout of Pseudouridine synthase 1 (PUS1) in mice. [Liver]

Project description:In an effort to produce a mouse model of Mitochondrial Myopathy with Lactic acidosis and Sideroblastic Anemia (MLASA), we knocked out the gene for Pseudouridine synthase 1 (PUS1), an enzyme that modifies uridine to pseudouridine in many cytoplasmic and mitochondrial tRNAs, as well as other cellular RNAs. The Pus1-/- mice are viable, are born at the expected Mendelian frequency, and are non-dysmorphic. The PUS1 mRNA and certain pseudouridine modifications are absent in cytoplasmic and mitochondrial tRNAs in the Pus1-/- mice. The Pus1-/- mice display reduce exercise capacity at 14 weeks, with alterations in muscle morphology, histology, and physiology. Red gastrocnemius muscle from Pus1-/- mice shows reduced number and size of mitochondria and reduced Cytochrome C oxidase activity. Two-condition, two-color experiment: Mouse wild type PUS1 and homozygous mutant PUS1 liver tissue samples: 4 biological replicates each.

2016-05-16 | E-GEOD-77820 | biostudies-arrayexpress

Knockout of Pseudouridine synthase 1 (PUS1) in mice. [Heart]

Project description:In an effort to produce a mouse model of Mitochondrial Myopathy with Lactic acidosis and Sideroblastic Anemia (MLASA), we knocked out the gene for Pseudouridine synthase 1 (PUS1), an enzyme that modifies uridine to pseudouridine in many cytoplasmic and mitochondrial tRNAs, as well as other cellular RNAs. The Pus1-/- mice are viable, are born at the expected Mendelian frequency, and are non-dysmorphic. The PUS1 mRNA and certain pseudouridine modifications are absent in cytoplasmic and mitochondrial tRNAs in the Pus1-/- mice. The Pus1-/- mice display reduce exercise capacity at 14 weeks, with alterations in muscle morphology, histology, and physiology. Red gastrocnemius muscle from Pus1-/- mice shows reduced number and size of mitochondria and reduced Cytochrome C oxidase activity. Two-condition, two-color experiment: Mouse wild type PUS1 and homozygous mutant PUS1 heart tissue samples: 4 biological replicates each.

2016-05-16 | E-GEOD-77818 | biostudies-arrayexpress

Knockout of Pseudouridine synthase 1 (PUS1) in mice. [Brain]

Project description:In an effort to produce a mouse model of Mitochondrial Myopathy with Lactic acidosis and Sideroblastic Anemia (MLASA), we knocked out the gene for Pseudouridine synthase 1 (PUS1), an enzyme that modifies uridine to pseudouridine in many cytoplasmic and mitochondrial tRNAs, as well as other cellular RNAs. The Pus1-/- mice are viable, are born at the expected Mendelian frequency, and are non-dysmorphic. The PUS1 mRNA and certain pseudouridine modifications are absent in cytoplasmic and mitochondrial tRNAs in the Pus1-/- mice. The Pus1-/- mice display reduce exercise capacity at 14 weeks, with alterations in muscle morphology, histology, and physiology. Red gastrocnemius muscle from Pus1-/- mice shows reduced number and size of mitochondria and reduced Cytochrome C oxidase activity. Two-condition, two-color experiment: Mouse wild type PUS1 and homozygous mutant PUS1 brain tissue samples: 4 biological replicates each.

2016-05-16 | E-GEOD-77817 | biostudies-arrayexpress

Exonuclease-assisted identification of pseudouridine sites in single-stranded RNA

Project description:Pseudouridine is considered as the most abundant modified nucleotides in RNA, playing an indispensable role in various life processes. The identification of pseudouridine sites provides the basis for the study of their function. Here, we proposed a new method for the identification of pseudouridine sites with a higher signal-to-noise ratio, combining CMC-specific labeling of pseudouridine sites and exonuclease-assisted strategy. We called this method exonuclease-assisted identification of pseudouridine sites (EAIPS).

2024-11-06 | GSE229317 | GEO

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