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样本的植物材料。表S2. Iso-seq文库的读数统计。表S3A和B. 在位置L1至L30处具有测序误匹配的剪接位点的数量和百分比，其中A)上游（左侧）和B)下游（右侧）的剪接位点。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. 验证TSS和TES位点的序列基序。表S7. 每个Iso-seq文库对AtIso贡献的基因和转录本数量。表S8. 随着每个文库的添加，AtIso中独特基因和转录本数量的饱和曲线。表S9. AtRTD3 - 来自TransFeat的转录本特征及其翻译。表S10A. AtRTD3针对单外显子/多外显子基因以及具有单个或多个转录本等位基因的基因的TranSuite输出；B) AtRTD3基因和转录本特征比较的TranSuite输出。表S11. AtRTD3 - 新基因。表S12. 使用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基因的基因描述。