GSM5577327: P. gingivalis cultured in medium [J_2]; Porphyromonas gingivalis ATCC 33277; RNA-Seq
Total RNA was isolated from the samples using TRIzol® reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocols. Further, genomic DNA was removed using the commercially available DNase I system (Qiagen, Germantown, PA, USA), and RNA concentration was realized by determining the A260/A280 ratio using a Nanodrop 2000 system (ThermoFisher, Waltham, MA, USA). RNA integrity was verified via 1.5% agarose gel electrophoresis, and qualified RNAs were quantified using a Qubit 3.0 fluorometer with a QubitTM RNA Broad Range Assay Kit (ThermoFisher, Waltham, MA). Furthermore, the RNA samples were analyzed at the Huayin Genome Research Facility (Huayin Health Medical Group Co, Wuhan, China) to determine ribosomal RNA (rRNA) depletion and subsequent RNA sequencing, and rRNA was removed using a Ribo-off rRNA Depletion Kit (Vazyme Biotech Co., Nanjing, China) for humans (Catalog No. N406) and/or bacteria (catalog NO. N407). Additionally, cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA). RNA libraries were prepared for sequencing using standard Illumina protocols
GEO Accession
GSM5577327