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. Author manuscript; available in PMC: 2021 May 7.
Published in final edited form as: Nat Methods. 2020 Aug 31;17(10):991–1001. doi: 10.1038/s41592-020-0935-4

Extended Data Fig. 10. Benchmarking the 2nd SS scNT-Seq protocol in human K562 cells.

Extended Data Fig. 10

a. Bar plot showing nucleotide substitution rates in K562 cells analyzed with different experimental protocols. 4sU, metabolic labeling with 4sU (100 μM, 4 h); TFEA, on-bead TFEA/NaIO4 chemical reaction; 2nd SS, second strand synthesis.

b. PCA plots showing K562 cells colored by the total RNA level of the TOP2A gene (natural log transformation of (TP10K + 1)) in three experimental protocols (same as in Fig. 6d).

c. Violin plots showing the new-to-total RNA ratios of 8 representative cell-cycle genes in datasets generated by 2nd SS (4sU/TFEA/2nd SS, n =795 cells) or standard (4sU/TFEA, n = 533 cell) scNT-Seq protocols. See ‘Data visualization’ in the Methods for definitions of box-plot elements.

d. Same as in c but showing new and old RNA levels (natural log transformation of (TP10K + 1)).