Schott et al. 2021 (PRJNA649002)

General Details

Title nRibo-Seq timecourse in RAW264.7 cells
Organism
Number of Samples 18
Release Date 2020/07/27 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP273781
ENA SRP273781
GEO
BioProject PRJNA649002

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)
SRR12333553 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq untreated
SRR12333554 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333555 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333556 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333557 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333558 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333562 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333563 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333564 PRJNA649002 Mus musculus RAW264.7 Ribo-Seq
SRR12333572 PRJNA649002 Mus musculus mESC Ribo-Seq
SRR12333573 PRJNA649002 Mus musculus mESC Ribo-Seq
SRR12333574 PRJNA649002 Mus musculus mESC Ribo-Seq
SRR12333568 PRJNA649002 Mus musculus mESC Ribo-Seq
SRR12333569 PRJNA649002 Mus musculus mESC RNA-Seq
SRR12333570 PRJNA649002 Mus musculus mESC RNA-Seq
SRR12333571 PRJNA649002 Mus musculus mESC RNA-Seq
SRR12333575 PRJNA649002 Mus musculus mESC RNA-Seq
SRR12333576 PRJNA649002 Mus musculus mESC RNA-Seq
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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