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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE229507 | GEO | 2024/02/06

REPOSITORIES: GEO

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

Project description:To investigate the effect of labeling durations on quantification bias in nucleotide conversion RNA-seq, we labeled NIH cells with 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

2024-02-06 | GSE229506 | GEO

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

Project description:To investigate the effect of increasing 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq, we labeled 3 different cell lines with increasing concentrations of 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

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

Project description:Effect of 4sU labeling on quantification bias in nucleotide conversion RNA-seq data

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

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

| PRJNA954792 | ENA

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

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

| PRJNA954793 | ENA

Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of TUC-seq versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq, we performed SLAM-seq and TUC-seq on NIH cells. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

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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

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

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Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

Project description:Effect of TUC-seq protocol versus SLAM-seq on quantification bias in nucleotide conversion RNA-seq data

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Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.

Project description:RNA synthesis and decay rates determine the steady-state levels of cellular RNAs. Metabolic tagging of newly transcribed RNA by 4-thiouridine (4sU) can reveal the relative contributions of RNA synthesis and decay rates. The kinetics of RNA processing, however, had so far remained unresolved. Here, we show that ultrashort 4sU-tagging not only provides snapshot pictures of eukaryotic gene expression but, when combined with progressive 4sU-tagging and RNA-seq, reveals global RNA processing kinetics at nucleotide resolution. Using this method, we identified classes of rapidly and slowly spliced/degraded introns. Interestingly, each class of splicing kinetics was characterized by a distinct association with intron length, gene length, and splice site strength. For a large group of introns, we also observed long lasting retention in the primary transcript, but efficient secondary splicing or degradation at later time points. Finally, we show that processing of most, but not all small nucleolar (sno)RNA-containing introns is remarkably inefficient with the majority of introns being spliced and degraded rather than processed into mature snoRNAs. In summary, our study yields unparalleled insights into the kinetics of RNA processing and provides the tools to study molecular mechanisms of RNA processing and their contribution to the regulation of gene expression.

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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

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

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