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In addition to the gene-level agreement between the Illumina and Ion Torrent platforms, they also showed similarity with respect to reads mapping to ribosomal RNA (rRNA)—commonly present even after poly-A selection—and the mitochondrial chromosome (chrM). Both platforms identified a down-regulation of reads mapping to chrM in the mice treated with IL-1β (Additional file 8: Figure S4, top), although the effect was more subtle in the Ion Torrent data. This falls in line with previous findings that IL-1β affects mitochondrial function in the liver, inhibiting hepatic ATP production [20]. Neither platform showed a treatment-specific effect in the number of rRNA reads (Additional file 8: Figure S4, bottom), though Ion Torrent tended to have a smaller percentage of rRNA-mapping reads than Illumina. Again, these patterns are present in data mapped by each alignment algorithm. Taken together, these results suggest the two sequencing platforms agree substantially at the level of alignments and gene quantification. Blair K. Ion Proton RNA-Seq: in search of the best alignment method – Seven Bridges [Internet]. Seven Bridg. 2014 [cited 2016 Sep 4]. Available from. Top 10 results from Ingenuity Pathway Analysis — Upstream Regulators. IPA results from the upstream regulators pathway analysis for each combination of platform and aligner. Table lists the identities of the upstream regulators, predicted activation state, p-value for DEG overlap with regulator targets, list of DEGs for each upstream regulator. (XLSX 19 kb).

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Li J, Tibshirani R. Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res. 2013;22:519–36.

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Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet. 2016;17:257–71. Read count and differential expression results for all combinations of platform/aligner. Gene-level read counts from each sample, p-values from the Mann-Whitney U tests and limma for differential expression, Benjamini-Hochberg-corrected q-values. (XLSX 13131 kb).

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Spearman and Pearson correlation coefficients for Illumina vs Ion Torrent fold-change comparison. Spearman and Pearson correlation coefficients between Illumina and Ion Torrent log2 fold-change values, within each alignment algorithm. Separate correlation coefficients were calculated for DEGs identified by both platforms, by Illumina only, and by Ion Torrent only. (XLSX 9 kb).

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Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30:434–9.

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Significant results from Ingenuity Pathway Analysis — Canonical Pathways. IPA results from the canonical pathways analysis for each combination of platform and aligner. Table lists pathway names, enrichment p-values, z-scores, and the list of DEGs for each pathway. (XLSX 35 kb).

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The owner of this website (has banned the autonomous system number (ASN) your IP address is in (9009) from accessing this website. Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. The authors declare no competing financial interests.

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Ensembl biotypes of genes detected by both platforms, or exclusively by one platform. For each aligner, lists the number of and percent of detected genes for each ensembl biotype. These numbers are broken down by those genes detected in both platform, only in Illumina data, and only in Ion Torrent. (XLSX 12 kb). Disclaimer: EBOOKEE is a search engine of ebooks on the Internet (4shared Mediafire Rapidshare) and does not upload or store any files on its server. Please contact the content providers to delete files if any and email us, we’ll remove relevant links or contents immediately. Looking specifically at the DEGs, we compared the length, number of exons, average exon length, and GC content of genes identified by both platforms, Illumina only, Ion Torrent only, and neither platform. While there were no differences in the majority of these metrics between these groups of DEGs, we did observe a trend in the GC content (Additional file 18: Figure S9). The DEGs detected in both platforms had a GC content centered on 50%, while the Illumina- and Ion Torrent-specific DEGs tended to have lower and higher GC contents, respectively. Both platforms have known GC biases [1, 29, 30] which could be contributing to these platform-specific differences.

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Prior studies have compared these two sequencing platforms for various applications including genome sequencing, RNA-Seq, and microbiome profiling [1,2,3,4,5]. These studies provide a basic indication of the error rates and reproducibility these platforms achieve, however there are two motivations for performing the present analysis. Baruzzo G, Hayer KE, Kim EJ, Di Camillo B, FitzGerald GA, Grant GR. Simulation-based comprehensive benchmarking of RNA-seq aligners. Nat Methods. 2016;14:135–39.

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