RNA work can be tricky at first, but you're on the right track. Here’s a quick guide to help you with collecting and storing bacterial cultures for RNA transcriptomics:

• Grow your cultures under standardized conditions (usually harvest at mid-log phase, OD600 ~0.4–0.6).

• Immediately stabilize RNA after sampling using:

• RNAprotect Bacteria Reagent (Qiagen) – add 2:1 (reagent to culture), incubate 5 min, then spin and freeze.

• Or, use fast filtration + flash freezing in liquid nitrogen (less expensive, but needs practice).

• Pellet cells quickly, keep samples on ice during processing.

• Store pellets at -80°C, and avoid freeze-thaw cycles.

• Use a bacteria-specific RNA extraction kit (e.g., RNeasy, Zymo).

• Include DNase digestion and check RNA quality using Bioanalyzer or TapeStation (RIN > 7 is ideal).

My personal recommendations:

• Qiagen’s RNAprotect Bacteria Reagent for stabilization.

• Zymo’s RNA Miniprep Kit for extraction.

• Bead beating + lysozyme if you're working with Gram-positive strains.

• Use Qubit for accurate RNA quantification, and always work RNase-free.

Best of luck with your RNA-seq project

Dr Muhammed Abdullahi

Thanks so much for your suggestions!