RNA October 2020 PMID 32503920

Nuclease-mediated depletion biases in ribosome footprint profiling libraries.

Boris Zinshteyn, Jamie R Wangen, Boyang Hua, Rachel Green

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Mentions

Peak: 4 in Jun 2020

across 3 sources since Apr 2020

Extended reach

158,330

potential audience

Total likes

Video views

3,659

Mentions per month

Apr 2020 – May 2023

Where it's discussed

X / Twitter7 posts
YouTube2 videos
Facebook2 posts

AI synopsis

What people are saying

The discussions reveal strong interest and engagement, with posts emphasizing the unsuitability of commercial rRNA removal products for footprint profiling and advocating for the use of custom oligos. Phrases like 'generally unsuitable' and 'recommend the use of' demonstrate a critical and constructive tone, indicating that the article prompts meaningful consideration of methodological improvements.

AgreementModerate agreement

Most discussions acknowledge the article’s findings, with some recommending specific methodological changes like using custom-designed oligos.

InterestHigh interest

Participants show high curiosity about the implications of the biases and the technical details, indicating strong engagement with the subject.

EngagementHigh engagement

Comments include evaluations of experimental approaches and practical recommendations, reflecting deep involvement.

ImpactModerate impact

The discussions highlight the potential influence on future research practices, though the overall recognition of broader impact remains moderate.

Abstract in brief

Ribosome footprint profiling is a technique used to study translation in cells, but it requires removing abundant ribosomal RNA (rRNA) to be effective.
Commercial rRNA removal products like RiboZero are no longer available, leading researchers to test alternatives, which are often not suitable for footprint profiling.
The recommended approach is to use custom-designed biotinylated oligos for rRNA removal, while solutions based on targeted nucleases are discouraged because they disrupt the detailed information needed for high-resolution analysis.]

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All mentions

Methods for Ribosomal RNA Depletion in Sequencing Applications

Ribosomal RNA can interfere with sequencing; this video discusses methods to effectively remove rRNA using DNA probes and hybridization strategies, crucial for accurate ribosome profiling.

the bumbling biochemist · Apr 20, 2022 2,226 views

Effective rRNA Depletion Methods for Sequencing Library Preparation

Ribosomal RNA can interfere with sequencing, requiring removal. Methods include using DNA probes with RNaseH or biotinylated probes with magnetic beads. Custom oligos are recommended for high-resolution footprint…

the bumbling biochemist · May 24, 2023 1,433 views

Current Protocols

@Curr_Protocols · X

RT @aemonten: "We evaluated several commercially available alternatives designed for RNAseq of human samples and find them generally unsuit…

Sep 16, 2020 · 2 shares · 2,197 followers View post →

Alejandro Montenegro

@aemonten · X

Sep 16, 2020 · 1 like · 2 shares · 9,046 followers View post →

Adam Hockenberry

@HockenberryAdam · X

RT @ribosome_papers: Pubmed: Nuclease-mediated depletion biases in ribosome footprint profiling libraries. https://t.co/jWCvjENeGY

Jun 8, 2020 · 1 share · 528 followers View post →

Fabrice Leclerc

@rnomics · X

Top #tweeted #RNA list story: Nuclease-mediated Depletion Biases in Ribosome Footprint Profiling Libraries - PubMed https://t.co/BL8OAaayr6, see more https://t.co/QRe3vIMZc3

Jun 8, 2020 · 2,759 followers View post →

Ribosome Papers

@ribosome_papers · X

Pubmed: Nuclease-mediated depletion biases in ribosome footprint profiling libraries. https://t.co/jWCvjENeGY

Jun 8, 2020 · 10 likes · 1 share · 2,927 followers View post →

papersformax

@papers_for_max · X

Nuclease-mediated depletion biases in ribosome footprint profiling libraries. https://t.co/vh4pvZVXVu

Jun 7, 2020 · 28 followers View post →

bioRxiv

@biorxivpreprint · X

Nuclease-mediated depletion biases in ribosome footprint profiling libraries https://t.co/mTTUyX20Qq #bioRxiv

Apr 1, 2020 · 137,175 followers View post →