Analysis of RNA polymerase stalling index in wild type and the rel- strain of Synechococcus elongatus PCC7942 - chromatin immunoprecipitation followed by sequencing during exposure to darkness (cells grown in light/dark conditions)

We investigated the role of ppGpp in Synechococcus elongatus PCC7942 in light/dark conditions. We performed ChIP-seq experiments using wild type and the rel- strain at dusk, during exposure to 12 h of darkness and at dawn. We show that the RNA polymerase pausing index is globally lower in the rel- strain. Enriched mRNA was prepared from synchronized S. elongatus cells at indicated time points using the Illumina TruSeq Stranded mRNA Sample Prep Kit and Illumina HiSeq technology.