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Series GSE150286 Query DataSets for GSE150286
Status Public on May 12, 2020
Title Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Over the past decade, experimental procedures such as metabolic labeling for determining RNA turnover rates at the transcriptome-wide scale have been widely adopted. Several computational methods to estimate RNA processing and degradation rates from such experiments have been suggested, but they all require several RNA sequencing samples. Here we present a method that can estimate RNA processing and degradation rates from a single sample. To this end, we use the Zeisel model and take advantage of its analytical solution, reducing the problem to solving a univariate non-linear equation on a bounded domain. The approach is computationally rapid and enables inference of rates that correlate well with previously published datasets. In addition to saving experimental work and computational time, having a sample-based rate estimation has several advantages. It does not require an error-prone normalization across samples and enables the use of replicates to estimate uncertainty and perform quality control. Finally the method and theoretical results described here are general enough to be useful in other settings such as nucleotide conversion methods.
Overall design Wildtype mouse embryonic stem cells (mESCs) were labeled with 4-thiouridine for 10 minutes. Biochemical separation was then used to separate the pool of transcripts containing 4sU (newly transcribed RNA) from the preexisting RNA. Newly transcribed and preexisting RNA were sequenced on Illumina HiSeq 2500.
Contributor(s) Hersch M, Biasini A, Marques AC, Bergmann S
Citation(s) 35459101
Submission date May 11, 2020
Last update date May 05, 2022
Contact name Ana Marques
Organization name University of Lausanne
Department Department of Computational Biology
Street address Rue du Bugnon 27
City Lausanne
ZIP/Postal code 1005
Country Switzerland
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (2)
GSM4544779 WT_10min_lab
GSM4544780 WT_10min_tot
BioProject PRJNA631723
SRA SRP261115

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Supplementary file Size Download File type/resource
GSE150286_4sU_TPM_table.txt.gz 1.7 Mb (ftp)(http) TXT
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