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Effect of performing SLAM-seq chemistry in methanol fixed cells versus standard tube processing on quantification bias in nucleotide conversion RNA-seq data

ABSTRACT: To investigate the occuring 4sU dropout during library preparation we performed SLAM conversion either in intact, methanol fixed cells or in tubes

ORGANISM(S): Mus musculus

PROVIDER: GSE253370 | GEO | 2024/02/06

REPOSITORIES: GEO

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Effect of 4sU labeling durations on quantification bias in nucleotide conversion RNA-seq data

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Effect of 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq data

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SLAM-Seq analysis of Ythdf2-deficient pre-leukemic cells

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Project description:We recently showed that methanol emitted by wounded plants might function as a signaling molecule for plant-to-plant and plant-to-animal communications. In mammals, methanol is considered a poison because the enzyme alcohol dehydrogenase (ADH) converts methanol into toxic formaldehyde. However, the detection of methanol in the blood and exhaled air of healthy volunteers suggests that methanol may be a chemical with specific functions rather than a metabolic waste product. Using a genome-wide analysis of the mouse brain, we demonstrated that an increase in blood methanol concentration led to a change in the accumulation of mRNAs from genes primarily involved in detoxification processes and regulation of the alcohol/aldehyde dehydrogenases gene cluster. Removal of the intestine significantly decreased the rate of methanol addition to the plasma and suggested that the gut flora may be involved in the endogenous production of methanol. Liver mRNA quantification showed changes in the accumulation of mRNAs from genes involved in cell signalling and detoxification processes. We hypothesized that endogenous methanol acts as a regulator of homeostasis by controlling the mRNA synthesis

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