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