Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite

Data necessary to reproduce figures in manuscript titled "Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite". Includes: Compressed arrow dataset used to produce Figure S6 (subtlseq_dataset.tar) Annotations used to process data (Hs_ensembl_lvl1_and_2.gtf and Hs_ensembl.gtf) Processed data to produce Figures 3C and S2 (cB_ensembl_totRNAsubtlseq.csv.gz and cB_ensemblLvl1and2_totRNAsubtlseq.csv.gz, respectively). Simulated data originally used in bakR publication (Vock and Simon, 2023) used to make Figure 6 of EZbakR suite paper. Also includes supplemental tables of: List of genes producing transcripts predicting to undergo nuclear decay (PUNDs; Supplemental_Table_PUNDs.csv) Estimates for mature RNA synthesis, nuclear degradation, nuclear export, and cytoplasmic degradation rate constants from Ietswaart et al., 2024 total-cytoplasmic-nuclear TimeLapse-seq dataset (Supplemental_Table_NucCytoEsts.csv) Estimates for premature RNA synthesis, premature RNA processing, and mature RNA degreadation obtained from EZbakR analysis of Ietswaart et al., 2024 total RNA TimeLapse-seq dataset (Supplemental_Table_PtoMests.csv). Scripts to reproduce figures can be found at: https://github.com/isaacvock/EZbakRsuite_paper_code本数据集用于复现题为《借助EZbakR套件拓展并优化核苷酸重编码RNA测序实验的分析方法》的手稿中的图表，具体包含以下内容： 1. 用于生成补充图S6的压缩Arrow数据集（subtlseq_dataset.tar）； 2. 用于处理测序数据的基因注释文件：Hs_ensembl_lvl1_and_2.gtf与Hs_ensembl.gtf； 3. 用于生成图3C与补充图S2的已处理数据，分别为cB_ensembl_totRNAsubtlseq.csv.gz与cB_ensemblLvl1and2_totRNAsubtlseq.csv.gz； 4. 用于生成EZbakR套件论文图6的模拟数据，该数据最初发表于bakR论文（Vock与Simon，2023）。 此外，数据集还包含以下补充表格： 1. 预测会发生核降解的转录本编码基因列表（PUNDs；Supplemental_Table_PUNDs.csv）； 2. 基于Ietswaart等人2024年发布的全细胞-细胞质-细胞核时间流逝测序（TimeLapse-seq）数据集得到的成熟RNA合成、核降解、核输出及细胞质降解速率常数估算值（Supplemental_Table_NucCytoEsts.csv）； 3. 基于Ietswaart等人2024年发布的总RNA时间流逝测序（TimeLapse-seq）数据集的EZbakR分析结果，得到的前体RNA合成、前体RNA加工及成熟RNA降解速率常数估算值（Supplemental_Table_PtoMests.csv）。 复现所有图表的脚本可于以下网址获取：https://github.com/isaacvock/EZbakRsuite_paper_code