Supplemental Tables — A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

Supplemental Tables S1-S6. This is part of the supplemental material for the study entitled: "A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon" by Alan P. R. Lorenzetti, Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L. G. de Lomana, José V. Gomes-Filho, Ricardo Z. N. Vêncio, Robert L. Moritz, Tie Koide, and Nitin S. Baliga. Table S1 | Annotation sources for constructing the <em>Halobacterium salinarum</em> NRC-1 non-redundant transcriptome and a loci dictionary. Table S2 | Comparison of Pearson correlation coefficient computed for protein and mRNA abundance throughout the growth curve. We compared the coefficients using Zou’s confidence interval method implemented in the cocor package. Subscripts <em>P</em> and <em>m</em> refer to protein and mRNA levels for indicated time points. Uppercase letters (A-F) refer to panels in Figure 2. * Δ<em>R</em> stands for the subtraction between the two coefficients (e.g., <em>R</em>TP1(A) - <em>R</em>TP2(B)). A confidence interval (CI) of Δ<em>R</em> spanning zero is not significant. Coefficients diverge slightly from those presented in the main text due to technical differences between the comparative approach and classic correlation method implementations. TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase. Table S3 | The non-redundant set of insertion sequences in <em>Halobacterium salinarum</em> NRC-1. We obtained insertion sequence families from ISfinder and ISsaga, and the transposition mechanisms from Siguier et al. (2015). Table S4 | Summary of the transposition detection assay. ª Number of identified insertion clusters. b Number of identified excision clusters. c Number of reads aligned to the reference genome. d Sum of insertion and excision clusters normalized by the library with the highest number of aligned reads. Table S5 | List of primers used in this study. Table S6 | In-house and third-party GitHub repositories cited in this study.