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. Author manuscript; available in PMC: 2017 Jul 1.
Published in final edited form as: Methods. 2016 Apr 12;103:34–48. doi: 10.1016/j.ymeth.2016.04.002

Figure 2. Comparison of SHAPE-Seq v2.0 vs. v2.1 in vitro reactivities.

Figure 2

(A) Reactivity maps derived from the 5S rRNA from E. coli after equilibrium refolding and modification processed with either v2.0 (RMDB: 5SRRNA_1M7_0008) or v2.1 (RMDB: 5SRRNA_1M7_0009) library preparation steps. The reactivities closely agree, with a Pearson Correlation Coefficient (PCC) of 0.97. The ‘GGA’ sequence added to the 5′ end of the 5S rRNA to aid in vitro transcription is not shown, although included with PCC analysis. (B) The same analysis for the add adenine aptamer domain from V. vulnificus shows a PCC of 0.99 (RMDBs for v2.0: ADDSC_1M7_0007 and v2.1: ADDSC_1M7_0008). Like the 5S rRNA, a ‘GG’ sequence was added to aid in vitro transcription and is not shown on the graph, but is included in the PCC analysis.