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:

1. Compressed arrow dataset used to produce Figure S6 and S7 (subtlseq_data.tar.gz)
2. Compressed arrow dataset used to produce Figure 7 (subtlseq_perturbations_data.tar.gz)
3. eCLIP DDX3X peak calls from ENCODE used in Figure 7 (ENCFF901BYH_DDX3X_eCLIP.bed)
4. Annotations used to process data (Hs_ensembl_lvl1_and_2.gtf and Hs_ensembl.gtf)
5. Processed data to produce Figures 3C and S2 (cB_ensembl_totRNAsubtlseq.csv.gz and cB_ensemblLvl1and2_totRNAsubtlseq.csv.gz, respectively).
6. Simulated data originally used in bakR publication (Vock and Simon, 2023) used to make Figure 6 of EZbakR suite paper.
7. Processed data from the nanodynamo paper (Tarrerro et al. 2024) used to make Figure S9
8. Table from Ietswaart et al. 2024 of kinetic parameter estimates and PUND calls from that study (mmc2.xlsx)

Also includes supplemental tables of:

1. List of genes producing transcripts predicting to undergo nuclear decay (PUNDs; Supplemental_Table_PUNDs.csv)
2. 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)
3. 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

Updated to include data necessary to reproduce new figures/panels in revisions.