Correction to ‘Optimized design of antisense oligomers for targeted rRNA depletion’

Optimized design of antisense oligomers for targeted rRNA depletion

10.1101/2020.06.24.169102 ◽

2020 ◽

Author(s):

Wesley A. Phelps ◽

Anne E. Carlson ◽

Miler T. Lee

Keyword(s):

Ribosomal Rna ◽

Messenger Rna ◽

Optimized Design ◽

Rna Seq ◽

Web Tool ◽

Dna Oligomers ◽

Rrna Depletion ◽

Antisense Oligos ◽

Target Rna ◽

Oligo Design

ABSTRACTRNA sequencing (RNA-seq) has become a standard method for quantifying gene expression transcriptome-wide. Although RNA-seq is often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, selective rRNA digestion, using RNaseH and antisense DNA oligomers that tile the entire length of target RNAs, has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion method with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA, in a digestion reaction of only 5 minutes. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by designing oligo sets to deplete rRNA in Xenopus laevis and in zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to <5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.Abstract Figure

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Optimized design of antisense oligomers for targeted rRNA depletion

Nucleic Acids Research ◽

10.1093/nar/gkaa1072 ◽

2020 ◽

Author(s):

Wesley A Phelps ◽

Anne E Carlson ◽

Miler T Lee

Keyword(s):

Ribosomal Rna ◽

Messenger Rna ◽

Optimized Design ◽

Rna Seq ◽

Dna Oligomers ◽

Rrna Depletion ◽

Antisense Oligos ◽

Quantify Gene Expression ◽

Target Rna ◽

Oligo Design

Abstract RNA sequencing (RNA-seq) is extensively used to quantify gene expression transcriptome-wide. Although often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, digestion using RNaseH and antisense DNA oligomers tiling target rRNAs has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA in a 5-min digestion reaction. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by generating rRNA-depletion oligos for Xenopus laevis and for zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to <5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.

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Optimized Design Method of Microstrip Parallel-coupled Bandpass Filters with Compensation for Center Frequency Deviation

PIERS Online ◽

10.2529/piers041206062500 ◽

2005 ◽

Vol 1 (3) ◽

pp. 298-302 ◽

Cited By ~ 1

Author(s):

Houle Gan ◽

Dongxiao Yang ◽

Dongwu Lou

Keyword(s):

Design Method ◽

Bandpass Filters ◽

Frequency Deviation ◽

Center Frequency ◽

Optimized Design

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A summary of beach nourishment in China: The past decade of practices

Shore & Beach ◽

10.34237/1008836 ◽

2020 ◽

pp. 65-73

Author(s):

Gen Liu ◽

Feng Cai ◽

Hongshuai Qi ◽

Jianhui Liu ◽

Gang Lei ◽

...

Keyword(s):

Beach Nourishment ◽

Developed Countries ◽

Ecological Design ◽

Optimized Design ◽

Limited Information ◽

Personal Communications ◽

Design Considerations ◽

The Past ◽

Technological Advances ◽

Urban Beaches

Beach nourishment has been widely used for beach protection around the world. However, there is limited information about beach nourishment in China. This study offers an overview of beach nourishment practices, status and technological advances in China, based on the literature, reports, and personal communications. The results demonstrate that beach nourishment has been recognized as an effective and environmentally friendly measure to combat coastal erosion and has been increasingly adopted in China, especially in the past decade. The unique characteristics of coastal China resulted in a difference in beach nourishment between China and Western developed countries in terms of the types, objectives, and shapes of beach nourishment. For the types of nourishments in China, there were approximately the same number of restored beaches and newly constructed beaches. For fill sediment, homogeneous fill and heterogeneous fill comprised 51.1% and 48.9% of projects, respectively. The objective of beach nourishment was mainly to promote coastal tourism, and the shape of nourished beaches was dominated by headland bays. This study also indicated that China has achieved a number of technological advances in beach nourishment, including methods of beach nourishment on severely eroded coasts and muddy coasts, an optimized design of drain pipes involved in urban beaches, and ecological design considerations. From the past decade of practices, four aspects were proposed as considerations for future nourishment: sand sources, technique advances, ecological effects, and management of beach nourishments.

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Optimized design of high efficient voice coil actuator in deformable mirror

Chinese Journal of Liquid Crystals and Displays ◽

10.37188/yjyxs20203511.1110 ◽

2020 ◽

Vol 35 (11) ◽

pp. 1110-1119

Author(s):

Shuo CAO ◽

◽

Zhi-gao ZHANG ◽

Zhi-yun ZHAO ◽

Hu GU ◽

...

Keyword(s):

Deformable Mirror ◽

Optimized Design ◽

High Efficient ◽

Voice Coil Actuator

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Optimized design for in vitro experiment of electret transdermal patches

Academic Journal of Second Military Medical University ◽

10.3724/sp.j.1008.2009.00477 ◽

2009 ◽

Vol 29 (5) ◽

pp. 477-480

Author(s):

Hai-ying TENG ◽

Mao-hai SONG ◽

Liang CHENG ◽

Yu-xiu KONG ◽

Jian JIANG

Keyword(s):

Optimized Design ◽

Transdermal Patches

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Model Analysis and Optimization of BIM Technology in High-rise Shear Wall Residential Structure

MATEC Web of Conferences ◽

10.1051/matecconf/201926702001 ◽

2019 ◽

Vol 267 ◽

pp. 02001

Author(s):

Liangli Xiao ◽

Yan Liu ◽

Zhuang Du ◽

Zhao Yang ◽

Kai Xu

Keyword(s):

Structural Analysis ◽

Collaborative Design ◽

Structural Model ◽

Structural Information ◽

Shear Wall ◽

Structure Design ◽

Secondary Development ◽

Optimized Design ◽

Analysis Model ◽

High Rise

This study combines specific high-rise shear wall residential projects with the Revit to demonstrate BIM application processes. The use of R-Star CAD may help to realize the link barrier of the building information model and the structural analysis software PKPM. Sequentially, the information supplement of the structural analysis model is completed by extracting the structural information with the Revit secondary development. By the collaborative design platform based on BIM technology, the paper examines the collision check of structural model, conducts collision analysis on other professional models and modifies the design scheme for conflict points. After the statistics of material usage, an optimized design is proposed. The findings of this paper could contribute to provide some reference for the specific application of BIM in structural design and realize the application of BIM technology in the process of building structure design.

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