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Series GSE118121 Query DataSets for GSE118121
Status Public on Dec 31, 2019
Title Chemical nucleoside conversion-based measurement of RNA stability by targeted and untargeted mRNA 3ยด end sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Gene expression profiling by high-throughput sequencing determines changes in gene expression only at steady state but prevents our understanding of the underlying gene expression kinetics. Here, we describe a protocol that combines metabolic RNA labeling with thiol-specific chemical nucleoside conversion to determine the stability of polyadenylated RNA transcripts. And we provide a targeted mRNA 3 end library preparation protocol that enable to robustly determine the stability even of RNA transcripts that escape robust detection in untargeted libraries. The described methods enable cost-effective insights into the kinetics underlying steady-state gene expression in order to study the mechanisms underlying the regulation of gene expression at a transcript-specific and genomic scale.
Overall design Mouse embryonic stem cells (mES cells) were subjected to s4U metabolic RNA labeling for 12h, followed by washout and chase using non-thiol-containing uridine. Total RNA was prepared at various time points along the chase (0h, 0.5h, 1h, 3h, 6h, and 12h). Total RNA was then subjected to alkylation and targeted RNA-seq using custom-designed primers.
Contributor(s) Herzog VA, Fasching N, Ameres SL
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Submission date Aug 03, 2018
Last update date Jan 01, 2020
Contact name Brian Reichholf
Organization name IMBA
Lab Stefan Ameres
Street address Doktor-Bohr-Gasse 3
City Vienna
ZIP/Postal code 1030
Country Austria
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (14)
GSM3318873 mESC no s4U Rep 1
GSM3318874 mESC no s4U Rep 2
GSM3318875 mESC 0h chase Rep 1
BioProject PRJNA484507
SRA SRP156338

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Supplementary file Size Download File type/resource
GSE118121_RAW.tar 20.0 Kb (http)(custom) TAR (of TSV)
GSE118121_artificial_chromosome_targetedRNAseq.bed.gz 153 b (ftp)(http) BED
GSE118121_artificial_chromosome_targetedRNAseq.fa.gz 732 b (ftp)(http) FA
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Raw data are available in SRA
Processed data provided as supplementary file

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