Evidence map›Paper›PMID 30629669›Full record

ArticlePloS one2019

The validation of Short Interspersed Nuclear Elements (SINEs) as a RT-qPCR normalization strategy in a rodent model for temporal lobe epilepsy.

René A J Crans, Jana Janssens, Sofie Daelemans, Elise Wouters, Robrecht Raedt, Debby Van Dam, Peter P De Deyn, Kathleen Van Craenenbroeck, Christophe P Stove

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed, 1 pooled it
–field-weighted citation impact
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

6 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Article
  6. 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

9 authors.

René A J CransLaboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium.
Jana JanssensLaboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.
Sofie DaelemansLaboratory for Clinical and Experimental Neurophysiology, Neurobiology and Neuropsychology (LCEN3), Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.ORCID 0000-0002-2670-911X
Elise WoutersLaboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium.
Robrecht RaedtLaboratory for Clinical and Experimental Neurophysiology, Neurobiology and Neuropsychology (LCEN3), Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
Debby Van DamLaboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.ORCID 0000-0003-4739-6076
Peter P De DeynLaboratory of Neurochemistry and Behavior, Department of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.ORCID 0000-0002-2228-2964
Kathleen Van CraenenbroeckLaboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium.
Christophe P StoveLaboratory for GPCR Expression and Signal Transduction (L-GEST) - Laboratory of Toxicology, Department of Bioanalysis, Ghent University, Ghent, Belgium.ORCID 0000-0001-7126-348X

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundIn gene expression studies via RT-qPCR many conclusions are inferred by using reference genes. However, it is generally known that also reference genes could be differentially expressed between various tissue types, experimental conditions and animal models. An increasing amount of studies have been performed to validate the stability of reference genes. In this study, two rodent-specific Short Interspersed Nuclear Elements (SINEs), which are located throughout the transcriptome, were validated and assessed against nine reference genes in a model of Temporal Lobe Epilepsy (TLE). Two different brain regions (i.e. hippocampus and cortex) and two different disease stages (i.e. acute phase and chronic phase) of the systemic kainic acid rat model for TLE were analyzed by performing expression analyses with the geNorm and NormFinder algorithms. Finally, we performed a rank aggregation analysis and validated the reference genes and the rodent-specific SINEs (i.e. B elements) individually via Gfap gene expression.

resultsGeNorm ranked Hprt1, Pgk1 and Ywhaz as the most stable genes in the acute phase, while Gusb and B2m were ranked as the most unstable, being significantly upregulated. The two B elements were ranked as most stable for both brain regions in the chronic phase by geNorm. In contrast, NormFinder ranked the B1 element only once as second best in cortical tissue for the chronic phase. Interestingly, using only one of the two algorithms would have led to skewed conclusions. Finally, the rank aggregation method indicated the use of the B1 element as the best option to normalize target genes, independent of the disease progression and brain region. This result was supported by the expression profile of Gfap.

conclusionIn this study, we demonstrate the potential of implementing SINEs -notably the B1 element- as a stable normalization factor in a rodent model of TLE, independent of brain region or disease progression.

Indexed as

Short Interspersed Nucleotide ElementsTranscriptomeAnimalsBrainDisease Models, AnimalDisease ProgressionEpilepsy, Temporal LobeGene Expression ProfilingHippocampusMaleRats, Sprague-DawleyReal-Time Polymerase Chain Reaction

Identifiers

PMID30629669
PMCPMC6328105

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.