Additional file 1 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Additional file 1: Table S1. Plant material for RNA samples for Iso-Seq. Table S2. Read statistics for Iso-seq libraries. Table S3A and B. Number and percentage of splice junctions with sequencing mismatches in positions L1 to L30 for A) upstream (left) and B) downstream (right) of splice junctions. Table S4. Position Weight Matrix scores for consensus splice site sequences of introns. Table S5A and B. Filtering of SJs on basis of mismatches in each position. Table S6. Sequence motifs for validation of TSS and TES sites. Table S7. Number of genes and transcripts contributed to AtIso from each Iso-seq library. Table S8. Saturation curve of the number of unique genes and transcripts added to AtIso with the addition of each library. Table S9. AtRTD3 - Transcript characteristics and translations from TransFeat. Table S10A. TranSuite output of AtRTD3 for mono-exonic/multi-exonic genes with single or multiple transcript isoforms; B Comparison of TranSuite output of AtRTD3 gene and transcript characterisation. Table S11. AtRTD3 - novel genes. Table S12. Functional analysis of transcripts from novel genes in AtRTD3 with TRAPID 2.0. Table S13. AtRTD3 - Chimeric Genes and transcripts. Table S14. Frequency of AS event type among AtRTD3, AtIso and Araport11. Table S15A. Frequency of AS event type among AtRTD3, AtIso and Araport11. Table S15B. Gene descriptions of genes containing non-stop RNAs.

附加文件 1：表 S1. 用于 Iso-Seq 的 RNA 样本植物材料。表 S2. Iso-seq 库的读数统计。表 S3A 和 B. 在 L1 至 L30 位置发生测序误匹配的剪接位点的数量和百分比，A) 剪接位点上游（左侧）和B) 剪接位点下游（右侧）。表 S4. 内含子共识剪接位点序列的位置权重矩阵得分。表 S5A 和 B. 基于每个位置误匹配对剪接位点进行过滤。表 S6. 用于验证 TSS 和 TES 位点的序列基序。表 S7. 每个 Iso-seq 库对 AtIso 贡献的基因和转录本数量。表 S8. 随着每个库的添加，AtIso 中添加的独特基因和转录本数量的饱和曲线。表 S9. AtRTD3 - 来自 TransFeat 的转录本特性和翻译。表 S10A. AtRTD3 对于单外显子/多外显子基因具有单个或多个转录本等位形的 TranSuite 输出；B) AtRTD3 基因和转录本特征的 TranSuite 输出比较。表 S11. AtRTD3 - 新基因。表 S12. 利用 TRAPID 2.0 对 AtRTD3 中新型基因的转录本进行功能分析。表 S13. AtRTD3 - 杂合基因和转录本。表 S14. 在 AtRTD3、AtIso 和 Araport11 中 AS 事件类型的频率。表 S15A. 在 AtRTD3、AtIso 和 Araport11 中 AS 事件类型的频率。表 S15B. 含有非终止 RNA 的基因描述。