Transcriptome data of DN11 cells grown on benzoate under anaerobic conditions 2
The total RNA from DN11 cells grown on benzene and benzoate under anaerobic conditions were extracted using the RNeasy Mini Kit (Qiagen) per manufacturer`s recommendation. The extracted RNA samples were treated with RQ1 RNase-free DNase (Promega) following the manufacturer`s instructions. The DNase-treated RNA samples were purified using RNeasy Mini Kit. The RNA quality and quantity were initially assessed using DU 800 Spectrophotometer (Beckman Coulter). For more accurate assessment, the integrity and concentration of each RNA sample were evaluated with Qubit RNA HS assay kit using Qubit RNA HS assay kit (Life Technologies) on Qubit 4.0 Fluorometer and RNA 6000 Nano Kit (Agilent Technologies, Inc) on Agilent 2100 Bioanalyzer, respectively, following the manufacturers protocol. For mRNA isolation, Ribo-Zero rRNA Removal Kit (Illumina) was used to deplete rRNA from the total RNA samples according to manufacturers instructions. The integrity and concentration of the purified mRNA samples were evaluated on Qubit 4.0 Fluorometer using Qubit RNA HS assay kit (Life Technologies) and Agilent 2100 Bioanalyzer using RNA 6000 Pico Kit (Agilent Technologies, Inc), respectively, following the manufacturers protocol. The purified mRNA was fragmented and converted to cDNA library with TruSeq RNA sample Prep Kit v2 (Ilumina) following the Low Sample Protocol recommended by the vendor. The Kapa Library Quantification kit was used to quantify the size of the library on a qPCR (7300 Real Time PCR system) following the protocol described by the manufacturer. The quality of the library was assessed on Agilent 2100 Bioanalyzer using Agilent DNA High Sensitivity Kit (Agilent Technologies, Inc). Sequencing of pooled cDNA libraries were conducted on MiSeq instrument (Illumina) using MiSeq Reagent Kit v3 (paired-end, 150 cycle) (Illumina) following the manufacturers protocol.