Zinshteyn et al. 2020 (PRJNA613736)

General Details

Title Nuclease-mediated depletion biases in ribosome footprint profiling libraries
Organism
Number of Samples 26
Release Date 2020/03/20 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP253534
ENA SRP253534
GEO GSE147324
BioProject PRJNA613736

Publication

Title
Authors Zinshteyn B, Wangen JR, Hua B, Green R
Journal RNA (New York, N.Y.)
Publication Date 2020 Oct
Abstract Ribosome footprint profiling is a high-throughput sequencing-based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally very abundant, ribosomal RNA sequences that dominate libraries and increase sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued as a standalone product and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them generally unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments. © 2020 Zinshteyn et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
PMC PMC7491325
PMID 32503920
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR11362448 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362449 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362450 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362451 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362452 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362453 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362454 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362455 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362456 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362457 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362458 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362459 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362460 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362461 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362462 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362463 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362464 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362465 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362466 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362467 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362468 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362469 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362470 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362471 PRJNA613736 Homo sapiens K562 Ribo-Seq Cycloheximide
SRR11362472 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
SRR11362473 PRJNA613736 Homo sapiens HEK293 Ribo-Seq Cycloheximide
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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