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Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7

ABSTRACT: Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7

PROVIDER: PRJNA770345 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16292027.fastq.gz	Fastqsanger.gz
	SRR16292028.fastq.gz	Fastqsanger.gz
	SRR16292029.fastq.gz	Fastqsanger.gz
	SRR16292030.fastq.gz	Fastqsanger.gz

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Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7 II

Project description:Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7 II

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Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7

Project description:The goal of this study is to compare transcriptome-wide Nm-seq on the poly A+ RNA of wild-type Raw264.7 macrophages to transcriptome-wide Nm-seq on the poly A+ RNA of Raw264.7 macrophages after VSV infection . The Nm-seq profiles of wild-type Raw264.7 poly A+ RNA and VSV infected Raw264.7 poly A+ RNA were generated by deep sequencing using Illumina HiSeq4000 sequencer.

2022-04-05 | GSE185661 | GEO

Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7 II

Project description:The goal of this study is to compare transcriptome-wide Nm-seq on the poly A+ RNA of wild-type Raw264.7 macrophages to transcriptome-wide Nm-seq on the poly A+ RNA of Fbl+/- Raw264.7 macrophages . The Nm-seq profiles were generated by deep sequencing using Illumina HiSeq4000 sequencer.

2022-04-05 | GSE196271 | GEO

Nm-seq finds thousands of modified 2’-O-methylation sites in mRNA with base precision

Project description:Nm-seq maps 2'-O-methylation sites in human mRNA with base precision The ribose of rna nucleotides can be 2′-O-methylated (nm). despite advances in high-throughput detection, the inert chemical nature of nm still limits sensitivity and precludes mapping in mrna. We leveraged the differential reactivity of 2′-O-methylated and 2′-hydroxylated nucleosides to periodate oxidation to develop nm-seq, a sensitive method for transcriptome-wide mapping of nm with base precision. nm-seq uncovered thousands of nm sites in human mrna with features suggesting functional roles.

2017-05-15 | GSE90164 | GEO

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Project description:Nm-seq finds thousands of modified 2’-O-methylation sites in mRNA with base precision

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Identifying Ipr1 binding sites in RAW264.7 cells using ChIP-seq

Project description:Identifying Ipr1 binding sites in RAW264.7 cells using ChIP-seq

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LXR activation in RAW264.7 mouse macrophages expressing LXRalpha.

Project description:To identify novel LXR target genes, we conducted transcriptional profiling studies using RAW264.7 cells ectopically expressing LXRalpha Total RNA was isolated from RAW264.7 macrophages ectopically expressing LXRalpha as described in Venkateswaran et al. (2000); PNAS 97, 12097-12102. Cells were cultured with DMSO or GW3965 (1 μM) and LG268 (100 nM). Transcriptional profiling was performed at the UCLA microarray core facility using murine Affymetrix 430 2.0 microarrays.

2009-08-01 | E-GEOD-17088 | biostudies-arrayexpress

Nm-Mut-seq: The base-resolution quantitative method for mapping transcriptome-wide 2’-O-methylations

Project description:2’-O-methylation (Nm) is a prevalent post-transcriptional RNA modification present in many cellular RNAs and plays a critical role in modulating both the physical properties and regulation of eukaryotic RNAs. Studies of Nm modifications in RNA have long been hampered by a lack of effective mapping methods. Previously reported approaches can work well for detecting Nm modifications on abundant RNAs, but face challenges when applied to low-abundant RNAs, such as mRNA, lack stoichiometric information, and are challenged by issues of RNA sample degradation due to chemical treatment. Here, we present Nm-Mut-seq, a mutation signature-based Nm mapping method, which uses a custom reverse transcriptase (RT) that installs mutations at Am, Cm, and Gm-modified sites (Um is undetectable by this method). Our work provides a much-needed approach to detect Nm at base resolution in low abundant RNAs and to estimate the stoichiometry of each modified site transcriptome-wide.

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Project description:Gene expression profile of FABP4 treatment in RAW264.7 macrophages was examined to show a ligand (palmitic acid)-dependent and a ligand-independent effect of FABP4. RAW264.7 macrophages were treated with and without 200 nM recombinant FABP4 in the absence and presence of 0.2 mM palmitic acid.

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