Additional file 1: of SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Figures S1–S6. (PDF 3939 kb

Binary logistic regression model with in-hospital mortality as the dependent factor.

<p>Variables with significant associations with mortality were tested; for AKI stage, stage 1 was taken as the reference category. Hospital acquired AKI was compared with community acquired AKI that was used as the reference category.</p

Univariate associations between co-morbid conditions and mortality in patients with AKI.

<p>There were no associations with diabetes, diabetic complications or dementia.</p

Table of the most frequent primary cause of death stratified by AKI stage.

<p>Results are displayed as percentages with absolute numbers in parentheses.</p

Frequency chart demonstrating major disease categories causing death in patients with AKI.

<p>Frequency chart demonstrating major disease categories causing death in patients with AKI.</p

Table of the most frequent primary causes of death.

<p>Table of the most frequent primary causes of death.</p

Additional file 8: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

Sequence of all primers generated for this study, together with qPCR probes, amplification efficiencies, and primer/probe combinations used. Exon content of amplicons used for Northern analyses is also shown. For additional assays, see [7]. (XLSX 12 kb

Additional file 2: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

a-d. Gene Ontology analyses showing over and under-represented gene ontologies (biological process and molecular function) in genes differentially expressed between untreated time-points. Analyses were performed using the Panther classification system [73], with a Bonferroni correction for multiple testing. e. Genes differentially expressed between IGF-1 treated and untreated samples. List includes genes identified by comparision at each timepoint, and an all v all comparison. No significant genes were identified in the day 90 analysis. (XLSX 50 kb

Additional file 5: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

Gene Ontology analysis showing over and under-represented gene ontologies (biological process and molecular function) in parent loci of 239 significantly altered circRNAs. Analyses were performed using the Panther classification system [73], with a Bonferroni correction for multiple testing. (XLSX 11 kb

Additional file 6: of Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular

FIRRE exon junctions confirmed by amplicon sequencing. All reads were mapped against hg19 without reference to transcript annotation: Amplicons using convergent primer pairs and divergent primer pairs (to amplify circRNAs only) are shown separately. Canonical junctions were mapped using MapSplice [67], circRNA (back-splice) junctions were mapped using PTESFinder [46]. For details, see methods. Exon number is according to schema in Fig. 6b. Junction position (hg19), amplicons of origin, and junction frequencies, are given for all junctions. Only splices with a frequency of 1% or higher in each amplicon, identified either by MapSplice or PTESfinder, are reported. Canonical junctions present within the current FIRRE annotation are show in blue. All others are not present within current annotation. Off target junctions (presumed to be generated by illegitimate primer binding) are also shown. Data is for confirmation of junction presence within transcripts only: Junction frequency is affected by position relative to primer, size dependent amplification bias during Nextera indexing, and size dependent bias in cluster formation/resolution efficiencies during MiSeq sequencing. (XLSX 71 kb