Evidence map›Paper›PMID 32141472›Full record

ArticleGenetics and molecular biology2020

SSD - a free software for designing multimeric mono-, bi- and trivalent shRNAs.

Gabriel José de Carli, Abdon Troche Rotela, Greice Lubini, Danyel Fernandes Contiliani, Nidia Benítez Candia, Thiago S Depintor, Fabiano Carlos Pinto de Abreu, Zilá Luz Paulino Simões, Danilo Fernández Ríos, Tiago Campos Pereira

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genetics and molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.4field-weighted citation impact, top 41% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 5 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 2 institutions in 2 countries.

Gabriel José de CarliUniversidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0003-3689-4512
Abdon Troche RotelaUniversidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, San Lorenzo, Paraguay.ORCID http://orcid.org/0000-0001-7390-1780
Greice LubiniUniversidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Biologia, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0001-6640-3724
Danyel Fernandes ContilianiUniversidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0002-9225-3384
Nidia Benítez CandiaUniversidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, San Lorenzo, Paraguay.ORCID http://orcid.org/0000-0003-3677-9960
Thiago S DepintorUniversidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0003-2610-867X
Fabiano Carlos Pinto de AbreuUniversidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0003-0112-2520
Zilá Luz Paulino SimõesUniversidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0003-2363-6178
Danilo Fernández RíosUniversidad Nacional de Asunción, Facultad de Ciencias Exactas y Naturales, San Lorenzo, Paraguay.ORCID http://orcid.org/0000-0002-8394-532X
Tiago Campos PereiraUniversidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.ORCID http://orcid.org/0000-0003-2641-7966
Universidade de São Paulo · BRUniversidad Nacional de Asunción · PY

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

RNA interference (RNAi) is a powerful gene silencing technology, widely used in analyses of reverse genetics, development of therapeutic strategies and generation of biotechnological products. Here we present a free software tool for the rational design of RNAi effectors, named siRNA and shRNA designer (SSD). SSD incorporates our previously developed software Strand Analysis to construct template DNAs amenable for the large scale production of mono-, bi- and trivalent multimeric shRNAs, via in vitro rolling circle transcription. We tested SSD by creating a trivalent multimeric shRNA against the vitellogenin gene of Apis mellifera. RT-qPCR analysis revealed that our molecule promoted a decrease in more than 50% of the target mRNA, in a dose-dependent manner, when compared to the control group. Thus, SSD software allows the easy design of multimeric shRNAs, for single or multiple simultaneous knockdowns, which is especially interesting for studies involving large amounts of double-stranded molecules.

Identifiers

PMID32141472
PMCPMC7197978
OpenAlexW3009120065

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.