GSM6383068: 272NAG1; Bifidobacterium longum subsp. infantis; RNA-Seq
Bacteria cells were harvested at exponential phase and pelleted immediately by centrifugation at 12,000 × g for 1 min and resuspended in 1 ml of RNAlater Ambion (Thermo Fisher Scientific, Waltham, MA, USA), and incubated at 4 °C overnight and then stored at – 80 °C until further analysis. RNA isolation was performed using a Ambion RNAqueousTM kit (Thermo Fisher Scientific) following manufacturer instructions. An additional step of bead-beating for cell disruption (FastPrep-24TM 5G, MP Biomedicals Inc, Santa Ana, CA, USA) was added to the RNA isolation procedure. Total RNA was immediately treated with the Turbo DNase free kit (Ambion, Thermo Fisher Scientific). Total RNA was treated with Ribo-Zero rRNA Removal kit, Bacteria (Illumina, San Diego, CA, USA) to remove ribosomal RNA according to manufacturer instructions. The depleted RNA was purified with RNAeasy MinElute Cleanup kit (Qiagen, Valencia, CA, USA).  Whole transcriptome libraries were constructed using TruSeq Stranded mRNA Library Preparation Kit (Illumina) or NEBNext Ultra II Directional RNA library Prep Kit for Illumina (New England Biolabs Inc, MA, USA) following manufacturer instructions.