E-GEOD-54199 - Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)

Status
Released on 10 April 2014, last updated on 31 May 2014
Organism
Escherichia coli, Streptococcus pneumoniae
Samples (18)
Protocols (5)
Description
We show that treatment with HPUra (for S. pneumoniae) and trimethoprim (for E. coli) leads to a skewed gene dosage profile (increase around the origin of replication), which is also propagated to the transcriptome level. Kanamycin, however, does not have this effect. In case of S. pneumoniae this shift in gene dosage distribution leads to the population-wide activation of competence. Pairwise comparison of untreated to antibiotic-treated cells (either DNA-seq or RNA-seq). It was performed with deep sequencing, using an Illumina HiSeq 2000 machine with 100 bp read length. S. pneumoniae samples treated with kanamycin was analysed from a single sample, while all other conditions were from duplicate samples.
Experiment types
DNA-seq, RNA-seq of coding RNA 
Contacts
Jelle Slager <j.slager@rug.nl>, J Slager, J W Veening, L Attaiech, M Kjos
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-54199.idf.txt
Sample and data relationshipE-GEOD-54199.sdrf.txt
Links