E-MTAB-1901 - RNA-seq of coding RNA from salmonella enterica typhimurium wild-type or delta araC mutant cells grown in the presence or absence of 0.2% L-arabinose to determine the effects of AraC and arabinose on RNA levels genome-wide

Status
Released on 4 October 2013, last updated on 2 May 2014
Organism
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu
Samples (4)
Protocols (8)
Description
We used RNA-seq to determine the effects of AraC and arabinose on RNA levels genome-wide in S. enterica. Wild-type or delta araC mutant cells were grown in both the presence and absence of 0.2% L-arabinose. RNA-Seq libraries from two independent biological replicate samples were sequenced for (i) wild-type cells with no treatment, (ii) wild-type cells treated with arabinose, (iii) delta araC cells with no treatment, (iv) delta araC cells treated with arabinose. Comparisons were made between (i) and (ii) [analysis file name: Salmonella RNA-seq processed WT without arabinose vs WT with arabinose.xls], between (i) and (iii) [analysis file name: Salmonella RNA-Seq proessed no arabinose WT vs no arabinose delta araC.xls], and between (ii) and (iv) [analysis file name: Salmonella RNA-Seq processed arabinose WT vs arabinose delta araC.xls]. All analysis files are available from https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1901/E-MTAB-1901.additional.1.zip
Experiment types
RNA-seq of coding RNA, co-expression, in vivo, strain or line
Contact
Citation
Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon. Anne M. Stringer, Salvatore Currenti, Richard P. Bonocora, Catherine Baranowski, Brianna L. Petrone, Michael J. Palumbo, Andrew E. Reilly, Zhen Zhang, Ivan Erill, Joseph T. Wade. Journal of Bacteriology  (2014), Europe PMC 24272778
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-MTAB-1901.idf.txt
Sample and data relationshipE-MTAB-1901.sdrf.txt
Links