Additional file 2 of Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
Creators: name: Blumberg, Amit
name: Yixin Zhao
name: Huang, Yi-Fei
name: Dukler, Noah
name: Rice, Edward J.
name: Chivu, Alexandra G.
name: Krumholz, Katie
name: Danko, Charles G.
name: Siepel, Adam
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 2: Figure S1. Correlation of PRO-seq and RNA-seq replicates in K562 cells. Figure S2. Correlation of exonic reads from RNA-seq with either PRO-seq or intronic reads. Figures S3-S4. Scatter plots of PRO-seq vs. RNA-seq for intron-containing (Figure S3) or intron-less (Figure S4) transcription units in K562 cells. Figure S5. Scatter plots of PRO-seq vs. RNA-seq for lincRNAs and protein-coding mRNAs in K562 cells after matching by PRO-seq signal. Figures S6-S7. Scatter plots of PRO-seq vs. RNA-seq for transcription units in K562 cells (Figure S6) or HeLa cells (Figure S7). Figure S8. Scatter plots of PRO-seq vs. RNA-seq for mRNAs and lincRNAs in K562 cells before and after correcting for elongation rate. Figure S9. Intronic half-life vs. TimeLapse-seq half-life. Figure S10. Empirical cumulative distribution functions (eCDFs) for estimated half-lives of predicted targets of miR-125-5p and miR-19-3p vs. non-targets. Figure S11. Correlation of estimated RNA half-lives under various methods. Figure S12. Correlation of PRO-seq-based half-lives (T1/2PR, x-axis) vs. estimates from TimeLapse-seq (T1/2TLS, y-axis) after correcting for elongation rate. Figures S13-S14. SEM results for features of intron-containing (Figure S13) or intron-less (Figure S14) transcription units in K562. Figure S15. Estimated half-lives for intron-containing and intron-less transcription units. Figure S16. SEM results for features of intron-containing transcripts in K562 cells, with and without a correction for elongation rate. Figure S17. Multiple linear regression (MLR) for features of transcription units versus RNA stability in K562 cells. Figures S18-S19. DNA word enrichments in stable transcripts for protein-coding mRNAs (Figure S18) or lincRNAs (Figure S19). Figure S20. G+C content in intervals downstream of the TSS for various classes of transcription units. Figure S21. DNA word enrichments in stable transcripts for eRNAs. Figure S22. DNA methylation in lincRNAs of various stability levels. Figure S23. Sequence Stability Index of intron-containing versus intron-less genes. Figures S24-S25. Sequence Stability Index (SSI) for mRNAs (Figure S24) or lincRNAs (Figure S25) of various stability classes. Figures S26-S27. Histone modification signals for protein-coding mRNAs of various stability classes. Half-live estimations are based on published data (Figure S26) or newly collected data for this study (Figure S27). Figures S28-S29. Estimated SEM coefficients for transcription (λn; top) and half-life (μn; bottom) for 11 histone modifications. It’s assayed by ChIP-seq in the 500 bases (Figure S28) or 1000-1500 bases (Figure S29) downstream of the TSS. Figures S30-S31. Estimated SEM coefficients for transcription (λn; top) and half-life (μn; bottom) for 11 histone modifications. It’s based either on published data (Figure S30) or on the newly collected PRO-seq and RNA-seq data (Figure S31).