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M6A-SAC-seq for quantitative whole transcriptome m6A profiling

ABSTRACT: m6A-SAC-seq for quantitative whole transcriptome m6A profiling

PROVIDER: PRJNA814275 | ENA |

REPOSITORIES: ENA

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m6A-SAC-seq for quantitative whole transcriptome m6A profiling

Project description:This protocol describes a method for base-resolution, quantitative m6A sequencing in the whole transcriptome. The method generates highly reproducible results containing 31,233-129,263 sites using as low as 2 ng of poly-A RNA.

2022-06-30 | GSE198246 | GEO

SAC-seq for transcriptome-wide quantitative sequencing of mRNA m6A at base resolution

Project description:Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.

2024-04-19 | GSE243722 | GEO

Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [polyA_RNA]

Project description:We introduce m6A Selective Allyl Chemical labeling and Sequencing (m6A-SAC-Seq), a novel method for transcriptome-wide quantitative mapping of m6A at single-nucleotide resolution. The m6A-SAC-Seq employs a dimethyltransferase to selectively label m6A followed by introducing mutations with reverse transcriptase during sequencing. We identified the widespread distributions of m6A and quantitated their fractions in the transcriptome of HeLa, HEK293, HepG2, and human CD34+ hematopoietic stem/progenitor cells (HSPCs).

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Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [Ribo-minus_RNA]

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SAC-seq for transcriptome-wide quantitative sequencing of mRNA m6A at base resolution in Arabidopsis

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Quantitative and whole-transcriptome N6-Methyladenosine profiling at single-nucleotide resolution [shRNA RNA-seq]

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Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [III]

Project description:N6-methyladenosine (m6A) is the most abundant modification on mRNA, and is implicated in critical roles in development, physiology and disease. A major challenge in the field has been the inability to quantify m6A stoichiometry and the lack of antibody-independent methodologies for interrogating m6A. Here, we develop MASTER-seq for systematic quantitative profiling of m6A at single nucleotide resolution, building on differential cleavage by an RNAse at methylated sites. MASTER-seq permitted validation and de novo discovery of m6A sites, calibration of the performance of antibody based approaches, and quantitative tracking of m6A dynamics in yeast gametogenesis and mammalian differentiation. We discover that m6A stoichiometry is ‘hard-coded’ in cis via a simple and predictable code. This code accounts for ~50% of the variability in methylation levels and allows accurate prediction of m6A loss/acquisition events across evolution. MASTER-seq will allow quantitative investigation of m6A regulation in diverse cell types and disease states.

2019-07-01 | GSE129842 | GEO

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [II]

2019-07-01 | GSE122956 | GEO

Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution [I]

2019-07-01 | GSE122955 | GEO

m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome

Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

2016-06-24 | E-GEOD-66086 | biostudies-arrayexpress

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