Additional file 2 of Systematic discovery of subcellular RNA patterns in the gut epithelium

Additional files 2: Supplementary Tables 1-27. Table S1. Differential expression analysis results between DPP4 and GFP tethered APEX sequencing. Table S2. Categorized GO terms and Counts for the each categorized GO term. Table S3. GSEA of the APEX-seq data from DE results of DPP4. Table S4. Normalized gene counts of Mitochondria tagged samples. Table S5. Differential gene expression analysis results between ACTB and GFP and GO analysis results for ACTB enriched genes compared to GFP in APEX2 seq data. Table S6. Comparison between Apex2-seq and LCM data from [2]. Table S7. Z-score values of the selected transcripts from APEX sequencing. Table S8. smFISH quantification data using spot detection analysis. Table S9. smFISH quantification data of each ROI from the gradient spot detection analysis. Table S10. Quantification of diameter of RNA granules. Table S11. RBP-MS data comparison between Lct-3'UTR and Fluc. Table S12. RBP-MS data comparison between Net1-3'UTR and Fluc. Table S13. MERFISH 500 gene panel with barcode IDs. Table S14. Volume normalized MERFISH dot count differences between apical and basal sides of sIOs sections. Table S15. Shared gene list from UpSet plot on APEX-seq and sIOs-MERFISH data. Table S16. Wilcoxon test on sIOs-MERFISH data between apical and basal regions per gene. Table S17. Volume normalized MERFISH dot count differences between apical and basal sides of sIT sections. Table S18. Volume normalized MERFISH dot count for whole cell mass for sIT. Table S19. Venn diagram of sIOs and sIT (apical, basal and intersections). Table S20. Volume normalized MERFISH dot count differences between apical and basal sides of lIT sections. Table S21. Volume normalized MERFISH dot count for whole cell mass for lIT. Table S22. The scaled RNA-Protein plot with the GO categorization for villus Top and villus Bottom. Table S23. Plasmid IDs and sequences for APEX-seq and 3'UTR work. Table S24. qPCR results and primer information for mito APEX-seq. Table S25. Primer sequences for in vitro transcription. Table S26. Plasmid IDs and sequences for shRNA work. Table S27. qPCR results and primer information for shRNA work.

附加文件2：补充表1-27。表S1：DPP4与GFP锚定APEX测序（APEX sequencing）的差异表达分析结果。表S2：分类后的GO术语（GO terms）及各类GO术语的计数。表S3：基于DPP4差异表达结果的APEX测序数据的基因集富集分析（GSEA）结果。表S4：线粒体标记样本的标准化基因计数。表S5：APEX2测序（APEX2 sequencing）数据中，ACTB与GFP组的差异基因表达分析结果，以及ACTB富集基因相较于GFP组的GO分析结果。表S6：Apex2测序数据与文献[2]中的激光捕获显微切割（LCM, Laser Capture Microdissection）数据的对比分析。表S7：APEX测序筛选得到的转录本的Z得分（Z-score）。表S8：基于斑点检测分析的单分子荧光原位杂交（smFISH, single-molecule fluorescence in situ hybridization）定量数据。表S9：梯度斑点检测分析中各感兴趣区域（ROI, Region of Interest）的smFISH定量数据。表S10：RNA颗粒直径的定量分析结果。表S11：Lct-3'UTR与Fluc组的RNA结合蛋白质谱（RBP-MS, RNA-binding protein mass spectrometry）数据对比。表S12：Net1-3'UTR与Fluc组的RNA结合蛋白质谱数据对比。表S13：带有条形码ID的多重错误鲁棒荧光原位杂交（MERFISH, Multiplex Error-Robust Fluorescence In Situ Hybridization）500基因组合。表S14：sIOs切片的顶侧与基底侧的体积标准化MERFISH斑点计数差异。表S15：基于APEX测序与sIOs-MERFISH数据的UpSet图的共享基因列表。表S16：针对每个基因的sIOs-MERFISH数据，顶侧与基底侧区域的威尔科克森检验（Wilcoxon test）结果。表S17：sIT切片的顶侧与基底侧的体积标准化MERFISH斑点计数差异。表S18：sIT全细胞团的体积标准化MERFISH斑点计数。表S19：sIOs与sIT（顶侧、基底侧及交集区域）的韦恩图。表S20：lIT切片的顶侧与基底侧的体积标准化MERFISH斑点计数差异。表S21：lIT全细胞团的体积标准化MERFISH斑点计数。表S22：针对绒毛顶部与绒毛底部的缩放版RNA-蛋白关联图及GO分类结果。表S23：APEX测序与3'UTR相关实验的质粒ID及序列。表S24：线粒体APEX测序的定量聚合酶链反应（qPCR, quantitative polymerase chain reaction）结果及引物信息。表S25：体外转录所用引物的序列。表S26：短发夹RNA（shRNA, short hairpin RNA）相关实验的质粒ID及序列。表S27：shRNA相关实验的qPCR结果及引物信息。