Additional file 1 of Deep transcriptome profiling reveals limited conservation of A-to-I RNA editing in Xenopus
Creators: name: Nguyen, Tram Anh
name: Heng, Jia Wei Joel
name: Ng, Yan Ting
name: Sun, Rui
name: Fisher, Shira
name: Oguz, Gokce
name: Kaewsapsak, Pornchai
name: Xue, Shifeng
name: Reversade, Bruno
name: Ramasamy, Adaikalavan
name: Eisenberg, Eli
name: Tan, Meng How
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Fig. S1 Identification of RNA editing sites in X. laevis using publicly available Illumina RNA-seq data and our regular separate samples pipeline. Fig. S2 Distribution of mismatch types for recovered isolated sites in X. laevis identified using our regular separate samples pipeline. Fig. S3 Identification of RNA editing sites in X. laevis using publicly available Illumina RNA-seq data and our regular pooled samples pipeline. Fig. S4 Distribution of mismatch types for recovered isolated sites in X. laevis identified using our regular pooled samples pipeline. Fig. S5 Number of potential A-to-I editing sites in non-coding or coding regions after each step of filtering for all the X. laevis studies. Fig. S6 Identification of RNA editing sites in X. laevis using publicly available Illumina RNA-seq data and the hyper-editing pipeline. Fig. S7 Examples of dsRNA structures in repetitive regions of the X. laevis transcriptome. Fig. S8 Number of ADAR target sites per gene in X. laevis. Fig. S9 Individual A-to-I editing sites in our embryogenesis data. Fig. S10 ADAR expression and activity in embryogenesis data from the MK study. Fig. S11 Individual A-to-I editing sites in embryogenesis data from the MK study. Fig. S12 ADAR expression and activity in embryogenesis data from the DR study. Fig. S13 Individual A-to-I editing sites in embryogenesis data from the DR study. Fig. S14 Comparison of gene expression levels in X. laevis across studies. Fig. S15 Comparison of editing levels in X. laevis across studies. Fig. S16 Evaluation of different fold changes. Fig. S17 Correlation between editing levels of developmental process-specific sites and expression levels of the host genes. Fig. S18 Examples illustrating positive and negative relationships between A-to-I editing and gene expression. Fig. S19 Individual A-to-I editing sites in tissue data from the DR study. Fig. S20 Correlation between editing levels of tissue-specific sites and expression levels of the host genes. Fig. S21 Structure of the 3’UTR of cdc27. Fig. S22 Hierarchical clustering of genes containing two sites whose editing was significantly associated with each other (P &lt; 0.01, χ2-test). Fig. S23 Identification of A-to-I editing sites in X. tropicalis using RNA-seq data from the JBL study, where a total of 40 samples were analysed. Fig. S24 Identification of A-to-I editing sites in X. tropicalis using RNA-seq data from the MKK study, where a total of 193 samples were analysed. Fig. S25 Identification of A-to-I editing sites in X. tropicalis using RNA-seq data from the KW study, where a total of 6 samples were analysed. Fig. S26 Distribution of mismatch types for recovered isolated sites in X. tropicalis identified using our regular (A) separate samples or (B) pooled samples pipeline. Fig. S27 Number of potential A-to-I editing sites in non-coding or coding regions after each step of filtering for all the X. tropicalis studies. Fig. S28 Number of ADAR target sites per gene in X. tropicalis. Fig. S29 Examples of dsRNA structures in repetitive regions of the X. tropicalis transcriptome. Fig. S30 Individual A-to-I editing sites in embryogenesis data from the JBL study. Fig. S31 Gene expression analysis of embryogenesis data from the MKK study. Fig. S32 ADAR activity in embryogenesis data from the MKK study. Fig. S33 Individual A-to-I editing sites in embryogenesis data from the MKK study. Fig. S34 Hierarchical clustering of editing levels from the MKK study. Fig. S35 Examination of X. laevis editing sites in X. tropicalis. Fig. S36 Examination of X. tropicalis editing sites in X. laevis. Fig. S37 Cross-species comparison of editing rates for all matched sites. Fig. S38 Cross-species comparison of editing rates, omitting matched sites in genes with conflicting symbols. Fig. S39 Evaluation of X. laevis or X. tropicalis editing sites in X. andrei. Fig. S40 Distribution of mismatch types for coding regions in X. laevis. Fig. S41 Distribution of mismatch types for coding regions in X. tropicalis. Fig. S42 Types of coding mismatches identified by both regular read alignment and REDItools and the hyper-editing pipeline in X. laevis. Fig. S43 Types of coding mismatches identified by both regular read alignment and REDItools and the hyper-editing pipeline in X. tropicalis. Fig. S44 Developmental editing profiles of coding sites in Xenopus. Fig. S45. Profiles of high-confidence coding sites edited at 5% or higher in Xenopus. Fig. S46 High-confidence coding sites in X. laevis. Fig. S47 High-confidence coding sites in X. tropicalis. Fig. S48 Reasons for sites found in one species not detected in the other species. Fig. S49 Scatterplot showing the editing levels of high-confidence conserved coding sites in Xenopus. Fig. S50 Examination of human CDS sites in Xenopus. Fig. S51 Developmental editing profiles of conserved coding sites in Xenopus. Fig. S52 Editing profile of conserved coding sites in adult tissues of X. laevis.