7 protocols
AccessionNameType
P-MTAB-27625
data_generation
Illumina base calling using PHRED scoring for quality assesment
P-MTAB-27623
sequencing
Each library was loaded in a single lane and sequenced in a Ilumina GAIIx sequencer with a 36 cycles single read sequencing kit.
P-MTAB-27620
growth
Two flasks containing 10 mls of fresh Brucella Broth were (each one) inoculated with 2 mls of an overnight culture of Brucella abortus 2308.
P-MTAB-27621
specified_biomaterial_action
Erythritol was added at 1 mg/ml to one of them and both cultures were then allowed to grow during 2.5 h until an OD600 = 0.6-0.7
P-MTAB-27622
nucleic_acid_extraction
RNA was purified by using the Qiagen RNeasy Protect bacteria mini kit (Quiagen, USA)and RNase free DNase I digestion. Pure RNA (5 ug) was depleted of rRNA with the Ambion MICROBExpress kit.
P-MTAB-27626
 
High quality reads, 36 bp long, were aligned with the B. abortus 2308 reference genome (PRJNA62937ID) using MAQ allowing up to 2 missmatches. Number of reads were obtained with MAQ-pileup and converted to RPKM. Differential expression was assumed for a foldchange >2 between conditions.
P-MTAB-27624
library generation
Libraries were generated using the Illumina mRNA-seq sample preparation kit. Retrotranscribed dsDNA fragments of 200 bp were gel selected and amplified for 15 cycles