RNA from Wild type S. flexneri  strain 2457T without Congo Red supplementation
The NEB Next Ultra II RNA Library Prep Kit for Illumina (BioLabs, New England, MA, USA) was used for sequencing starting with the step of strand-specific library synthesis where the dTTPs were replaced by dUTPs during the synthesis of the second strand cDNA. The overhangs were converted to blunt ends, followed by adenylation of 3 ends and adapter ligation using RNA 5' and RNA 3' adapters included in the kit. Library concentration of 1.5 ng/ml was used after ensuring the insert size in a quality assessment prior to sequencing.