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 Halobacterium salinarum 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 P and m refer to protein and mRNA levels for indicated time points. Uppercase letters (A-F) refer to panels in Figure 2. * ΔR stands for the subtraction between the two coefficients (e.g., RTP1(A) - RTP2(B)). A confidence interval (CI) of ΔR 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 mobilome proteins in Halobacterium salinarum 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.