Supplementary data file 1 “genomeplot_WT_hetR_-N_chromosome.pdf”. Overview (chromosome) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type and hetR strain subjected to nitrogen deprivation for 0-6-12-24 hours as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 2 “genomeplot_WT_hetR_-N_plasmids.pdf”. Overview (six plasmids combined) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type and hetR strain subjected to nitrogen deprivation for 0-6-12-24 hours as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 3 “genomeplot_WT_+N_-N_chromosome.pdf”. Overview (chromosome) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type at 0 and 8 h after nitrogen depletion and at 0 and 8 h after NH4 addition as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 4 “genomeplot_WT_+N_-N_plasmids.pdf”. Overview (six plasmids combined) combining log2-normalized expression values (left y axis) from the microarray analysis of cultures of wild type at 0 and 8 h after nitrogen depletion and at 0 and 8 h after NH4 addition as indicated by coloured lines, with the reads numbers from the RNA-Seq dataset in (Mitschke, J., Vioque, A., Haas, F., Hess, W.R., and Muro-Pastor, A.M. (2011). Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc. Natl. Acad. Sci. USA 108, 20130-20135) (right y axis). Supplementary data file 5 “Co-expression network”. Cytoscape (www.cytoscape.org) file corresponding to the co-expression network constructed.

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