RIP-seq identification of RNAs enriched on RNA polymerase and the primary sigma factor (sigma A) in Bacillus subtilis

6S RNA is a small RNA with specific secondary structure that associates with the complex of RNA polymerase (RNAP) and the primary sigma factor in majority of bacteria. Bacillus subtilis has two 6S RNAs. To compare both 6S RNAs and to identify RNAs that might have a similar functions, we sequenced RNAs that co-immunoprecipitated with RNAP or the primary sigma factor (sigma A). We also sequenced total RNA isolated from the lysate (input sample). We expect that putative 6S RNA-like molecules are enriched in RNA polymerase or sigma A samples compared to the inputs. We performed the experiment both in exponential and stationary phase of growth.