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Journal articles
RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Abstract : Background: RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples-normal lung epithelium tissue and squamous cell carcinoma lung tumours. Protein coding mRNAs and long non-coding RNAs (lncRNAs) were included in the study. Results: Both platforms performed equally well for protein-coding RNAs, however the stochastic variability was higher for the sequencing data than for microarrays. This reduced the number of differentially expressed genes and genes with predictive potential for RNA-seq compared to microarray data. Analysis of this variability revealed a lack of reads for short and low abundant genes; lncRNAs, being shorter and less abundant RNAs, were found especially susceptible to this issue. A major difference between the two platforms was uncovered by analysis of alternatively spliced genes. Investigation of differential exon abundance showed insufficient reads for many exons and exon junctions in RNA-seq while the detection on the array platform was more stable. Nevertheless, we identified 207 genes which undergo alternative splicing and were consistently detected by both techniques.
Cited literature [62 references]
https://hal.univ-reims.fr/hal-02451663
Contributor : Valerian Dormoy <>
Submitted on : Wednesday, May 27, 2020 - 4:24:56 PM
Last modification on : Monday, May 17, 2021 - 2:52:23 PM
Contributor : Valerian Dormoy <>
Submitted on : Wednesday, May 27, 2020 - 4:24:56 PM
Last modification on : Monday, May 17, 2021 - 2:52:23 PM
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