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样本对应的植物材料；表S2：Iso-Seq文库的读段统计数据；表S3A与S3B：剪接接头上游（左侧）与下游（右侧）L1至L30位置存在测序错配的剪接接头的数量及占比；表S4：内含子共有剪接位点序列的位置权重矩阵（Position Weight Matrix, PWM）得分；表S5A与S5B：基于各位置错配情况对剪接接头（Splice Junctions, SJs）进行的过滤分析；表S6：用于验证转录起始位点（Transcription Start Site, TSS）与转录终止位点（Transcription End Site, TES）的序列基序；表S7：各Iso-Seq文库为AtIso贡献的基因与转录本数量；表S8：随文库逐步添加，新增至AtIso的特有基因与转录本数量的饱和曲线；表S9：AtRTD3——源自TransFeat的转录本特征与翻译结果；表S10A：针对携带单个或多个转录本亚型的单外显子/多外显子基因，AtRTD3的TranSuite输出结果；表S10B：AtRTD3基因与转录本特征的TranSuite输出结果对比；表S11：AtRTD3——新基因；表S12：利用TRAPID 2.0对AtRTD3中新基因的转录本开展的功能分析；表S13：AtRTD3——嵌合基因与转录本；表S14：AtRTD3、AtIso与Araport11中可变剪接（Alternative Splicing, AS）事件类型的发生频率；表S15A：AtRTD3、AtIso与Araport11中可变剪接事件类型的发生频率；表S15B：携带无终止RNA（non-stop RNAs）的基因的基因描述。