title: GSM4661062: RNA-Seq_Caulobacter_crescentus_NA1000 (WT)_rep1; Caulobacter vibrioides; RNA-Seq
library_construction_protocol: Cells were lysed in a Ready-Lyse lysozyme solution (Epicentre Technologies) according to manufacturer's instructions and lysates were homogenized through QiaShredder columns (Qiagen, Switzerland). The RNeasy Mini Kit (Qiagen, Switzerland) was used for total RNA extraction according to the manufacturer's protocol which included a first DNase treatment using the On-column DNase I digestion kit (Qiagen, Switzerland). Extracted total RNA was subjected to a second DNase treatment using Promega RQ1 at 1 unit/μg of RNA. Another total RNA cleanup was performed after the DNase treatment. The RNA concentration was measured using a Nanodrop 1000 spectrophotometer (ThermoScientific, USA) and RNA quality was assessed using a 2100 Bioanalyzer Instrument (Agilent Technologies, USA). RNA-Seq library preparation and sequencing was performed at Fasteris SA (Geneva, Switzerland). Bacterial rRNA were removed from each total RNA samples and RNA-Seq libraries were prepared using the Ovation Complete Prokaryotic RNA-Seq library system kit according to the manufacturer's instructions. Single-end runs were performed on an Illumina NextSeq 500 instrument (50 cycles), yielding several million reads (stored as fastq files). Using the web-based analysis platform Galaxy (https://usegalaxy.org), the single-end sequenced reads quality was checked (FastQC, Galaxy Version 0.72), and reads were mapped (Bowtie2, Galaxy Version 2.3.4.3) to the C. crescentus NA1000 genome (NC_011916.1). The tables of counts with the number of reads mapping to each gene feature were prepared using the htseq-count software, Galaxy Version 0.9.1. For each experimental series, the counts normalization and the statistical differential expression analysis was performed using the DESeq2 software, Galaxy Version 2.11.40.6.
attributes.tag: GEO Accession
attributes.value: GSM4661062