Evidence map›Paper›PMID 34674176›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing.

Nikoleta A Tzioutziou, Allan B James, Wenbin Guo, Cristiane P G Calixto, Runxuan Zhang, Hugh G Nimmo, John W S Brown

Open access · greenAbstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. 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
1.0field-weighted citation impact, top 23% 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, 3 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

7 authors at 3 institutions in 1 country.

Nikoleta A TzioutziouDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK.
Allan B JamesInstitute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
Wenbin GuoDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK.
Cristiane P G CalixtoDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK.
Runxuan ZhangInformation and Computational Sciences, The James Hutton Institute, Dundee, UK.
Hugh G NimmoInstitute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
John W S BrownDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, UK. j.w.s.brown@dundee.ac.uk.
James Hutton Institute · GBUniversity of Dundee · GBUniversity of Glasgow · GB

Funding

Biotechnology and Biological Sciences Research Council BB/K006835/1Biotechnology and Biological Sciences Research Council BB/P009751/1
6 · The paper itself

Abstract

RNA-sequencing (RNA-seq) is currently the method of choice for analysis of differential gene expression. To fully exploit the wealth of data generated from genome-wide transcriptomic approaches, the initial design of the experiment is of paramount importance. Biological rhythms in nature are pervasive and are driven by endogenous gene networks collectively known as circadian clocks. Measuring circadian gene expression requires time-course experiments which take into account time-of-day factors influencing variability in expression levels. We describe here an approach for characterizing diurnal changes in expression and alternative splicing for plants undergoing cooling. The method uses inexpensive everyday laboratory equipment and utilizes an RNA-seq application (3D RNA-seq) that can handle complex experimental designs and requires little or no prior bioinformatics expertise.

Indexed as

Alternative SplicingGene Expression ProfilingResearch DesignRNA-SeqSequence Analysis, RNATranscriptomeData validationExperimental designPrimer designRNA-seqTime course

Identifiers

PMID34674176
OpenAlexW3207126395

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.