Schott et al. 2021 (PRJNA720892)

General Details

Title nRibo-Seq timecourse in mESCs
Organism
Number of Samples 9
Release Date 2021/04/09 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP314203
ENA SRP314203
GEO
BioProject PRJNA720892

Publication

Title
Authors Schott J,Reitter S,Lindner D,Grosser J,Bruer M,Shenoy A,Geiger T,Mathes A,Dobreva G,Stoecklin G
Journal Nature methods
Publication Date 2021 Sep
Abstract In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way. © 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.
PMC
PMID 34480152
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR14195990 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195991 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195992 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195993 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195994 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195995 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195996 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195989 PRJNA720892 Mus musculus RAW264.7 Ribo-Seq
SRR14195997 PRJNA720892 Mus musculus RAW264.7 RNA-Seq untreated
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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