title: GSM4120362: ccrM2; Brevundimonas subvibrioides; RNA-Seq
library_construction_protocol: Total RNA from mid log stage cells was extracted using Max Bacterial Enhancement Reagent (Ambion) with TRIzol reagent (Ambion) and PureLink RNA Mini Kit (Invitrogen). The concentration was measured using a Nanodrop 2000 and sent for sequencing at the Center for Genomics and Bioinformatics at Indiana University, Bloomington. RNA integrity was assessed by an Agilent 2100 Bioanalyzer (Agilent Technologies). Messenger RNA enrichment was done by removing rRNA using MICROBExpress rRNA removal kit (Ambion). Before library preparation, cDNA was synthesized complementary to mRNA using random primers and Reverse Transcriptase. Second strands complementary to newly synthesized strands were synthesized, creating a double stranded DNA from the mRNA template. cDNA was used for library preparation using Nextera XT DNA Library Prep Kit (Illumina) followed by Illumina sequencing and analysis. After sequencing, raw reads were viewed by FASTQC, followed by adapter trimming and quality clipping by Trimmomatic and low-quality reads were discarded. Good quality reads were mapped to B. subvibrioides genome using Bowtie2. Differential gene expression analysis was performed using DEseq2 package.
attributes.tag: GEO Accession
attributes.value: GSM4120362