GSE111181
Differential RNA-Seq (dRNA-seq) data from Sphingopyxis granuli strain TFA grown in two different carbon sources and RNA-seq from Hfq-coIP experiment.
We performed differential RNA-sequencing (dRNA-seq) experiments in both minimal medium (MM) plus ß-hydroxybutyrate (ß-HB) and MM plus tetralin (THN) of Sphingopyxis granuli strain TFA. The objective was mapping the Transcription Start Site (TSS) of each gene in the genome in both conditions, detecting non-coding RNAs (ncRNAs) and comparing the gene expression profile in a preferential carbon source (ß-HB) versus tetralin (an aromatic pollutant). The dRNA-seq technique consists of using a termination exonuclease (TEX) to allow the discrimination of primary and processed transcripts. Furthermore, to detect Hfq-bound RNAs we co-immunoprecipitated RNA from the wild type strain (negative control) and a TFA strain with an Hfq-3xFlag tagged version (MPO501 strain) using an anti-3xFlag antibody and performed RNA-sequencing from the precipitated RNA. Overall design: Comparison of gene expression and TSS detection in TFA cells growing exponentially on minimal medium plus ß-hydroxybutyrate and minimal medium plus tetralin. Identification of Hfq-binding RNAs through a co-immunoprecipitation experiment.