Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Romero, Juan Pablo; Ortiz-Estévez, María; Muniategui, Ander; Carrancio, Soraya; Miguel, Fernando J. de; Carazo, Fernando; Montuenga, Luis M.; Loos, Remco; Pı́o, Rubén; Trotter, Matthew; Rubio, Ángel

doi:10.1186/s12864-018-5082-2

Cited by 19 publications

(13 citation statements)

References 40 publications

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“…Due to its specific design with specialized junction probes, the HTA2.0 microarray was more sensitive to known splicing events. Specialized junction arrays are generally described to be more performant than RNA-Seq [63]. Detection of differential splicing for RNA-Seq, however, relies on sequencing reads that cover a splicing site by chance [64].…”

Section: Discussionmentioning

confidence: 99%

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data

Vahlensieck

Thiel

Adelmann

et al. 2021

IJMS

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Cellular responses to micro- and hypergravity are rapid and complex and appear within the first few seconds of exposure. Transcriptomic analyses are a valuable tool to analyze these genome-wide cellular alterations. For a better understanding of the cellular dynamics upon altered gravity exposure, it is important to compare different time points. However, since most of the experiments are designed as endpoint measurements, the combination of cross-experiment meta-studies is inevitable. Microarray and RNA-Seq analyses are two of the main methods to study transcriptomics. In the field of altered gravity research, both methods are frequently used. However, the generation of these data sets is difficult and time-consuming and therefore the number of available data sets in this research field is limited. In this study, we investigated the comparability of microarray and RNA-Seq data and applied the results to a comparison of the transcriptomics dynamics between the hypergravity conditions during two real flight platforms and a centrifuge experiment to identify temporal adaptation processes. We performed a comparative study on an Affymetrix HTA2.0 microarray and a paired-end RNA-Seq data set originating from the same Jurkat T cell RNA samples from a short-term hypergravity experiment. The overall agreeability was high, with better sensitivity of the RNA-Seq analysis. The microarray data set showed weaknesses on the level of single upregulated genes, likely due to its normalization approach. On an aggregated level of biotypes, chromosomal distribution, and gene sets, both technologies performed equally well. The microarray showed better performance on the detection of altered gravity-related splicing events. We found that all initially altered transcripts fully adapted after 15 min to hypergravity and concluded that the altered gene expression response to hypergravity is transient and fully reversible. Based on the combined multiple-platform meta-analysis, we could demonstrate rapid transcriptional adaptation to hypergravity, the differential expression of the ATPase subunits ATP6V1A and ATP6V1D, and the cluster of differentiation (CD) molecules CD1E, CD2AP, CD46, CD47, CD53, CD69, CD96, CD164, and CD226 in hypergravity. We could experimentally demonstrate that it is possible to develop methodological evidence for the meta-analysis of individual data.

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Section: Discussionmentioning

confidence: 99%

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data

Vahlensieck

Thiel

Adelmann

et al. 2021

IJMS

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“…Although RNA-seq, a preferred platform for studying differentially expressed genes and alternative splicing nowadays, has some inherent advantages in comparison with microarrays, such as the ability to identify novel exons and splice junctions in an unbiased manner, the HTA 2.0 platform can nevertheless detect more weakly expressed events, which are missed in the RNA-seq results (Fumagalli et al, 2014 ; Wang et al, 2014 ; Romero et al, 2018 ). Furthermore, the modern microarrays, HTA 2.0, can still outperform RNA-seq for the analysis of gene expression in terms of cost, reproducibility and time as well as memory resources for treating data (Nazarov et al, 2017 ; Romero et al, 2018 ). For these reasons, we have chosen the HAT 2.0 platform as the major research approach for the AS studies.…”

Section: Discussionmentioning

confidence: 99%

The Study of Alternative Splicing Events in Human Induced Pluripotent Stem Cells From a Down's Syndrome Patient

Yang

Cai

et al. 2021

Front. Cell Dev. Biol.

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Down's syndrome (DS) is one of the most commonly known disorders with multiple congenital disabilities. Besides severe cognitive impairment and intellectual disability, individuals with DS also exhibit additional phenotypes of variable penetrance and severity, with one or more comorbid conditions, including Alzheimer's disease, congenital heart disease, or leukemia. Various vital genes and regulatory networks had been studied to reveal the pathogenesis of the disease. Nevertheless, very few studies have examined alternative splicing. Alternative splicing (AS) is a regulatory mechanism of gene expression when making one multi-exon protein-coding gene produce more than one unique mature mRNA. We employed the GeneChip Human Transcriptome Array 2.0 (HTA 2.0) for the global gene analysis with hiPSCs from DS and healthy individuals. Examining differentially expressed genes (DEGs) in these groups and focusing on specific transcripts with AS, 466 up-regulated and 722 down-regulated genes with AS events were identified. These genes were significantly enriched in biological processes, such as cell adhesion, cardiac muscle contraction, and immune response, through gene ontology (GO) analysis of DEGs. Candidate genes, such as FN1 were further explored for potentially playing a key role in DS. This study provides important insights into the potential role that AS plays in DS.

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“…Therefore, besides RNA-Seq, these data suggested that circRNA microarrays could be an efficient and sensitive tool for the profiling of specific circRNAs in tumor liquid biopsies. Moreover, Romero et al (2018) compared the performance of RNA-Seq and splice junction arrays for the analysis of transcript splicing events in breast cancer cell lines treated with a drug that affects splicing. They observed a high degree of coherence between the two technologies, with the detection power of the junction array being equivalent to RNA-Seq with up to 60 million reads.…”

Section: Discussionmentioning

confidence: 99%

Circular RNAs and RNA Splice Variants as Biomarkers for Prognosis and Therapeutic Response in the Liquid Biopsies of Lung Cancer Patients

et al. 2019

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Lung cancer, including non-small cell lung carcinoma (NSCLC), is the most frequently diagnosed cancer. It is also the leading cause of cancer-related mortality worldwide because of its late diagnosis and its resistance to therapies. Therefore, the identification of biomarkers for early diagnosis, prognosis, and monitoring of therapeutic response is urgently needed. Liquid biopsies, especially blood, are considered as promising tools to detect and quantify circulating cancer biomarkers. Cell-free circulating tumor DNA has been extensively studied. Recently, the possibility to detect and quantify RNAs in tumor biopsies, notably circulating cell-free RNAs, has gained great attention. RNA alternative splicing contributes to the proteome diversity through the biogenesis of several mRNA splice variants from the same pre-mRNA. Circular RNA (circRNA) is a new class of RNAs resulting from pre-mRNA back splicing. Owing to the development of high-throughput transcriptomic analyses, numerous RNA splice variants and, more recently, circRNAs have been identified and found to be differentially expressed in tumor patients compared to healthy controls. The contribution of some of these RNA splice variants and circRNAs to tumor progression, dissemination, or drug response has been clearly demonstrated in preclinical models. In this review, we discuss the potential of circRNAs and mRNA splice variants as candidate biomarkers for the prognosis and the therapeutic response of NSCLC in liquid biopsies.

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Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Cited by 19 publications

References 40 publications

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data

Rapid Transient Transcriptional Adaptation to Hypergravity in Jurkat T Cells Revealed by Comparative Analysis of Microarray and RNA-Seq Data

The Study of Alternative Splicing Events in Human Induced Pluripotent Stem Cells From a Down's Syndrome Patient

Circular RNAs and RNA Splice Variants as Biomarkers for Prognosis and Therapeutic Response in the Liquid Biopsies of Lung Cancer Patients

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