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E-GEOD-58891 - Transcriptome analysis of NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, NTHi 86-028NPrpsL∆fur∆hrrF, NTHi 86-028NPrpsL∆fur∆hrrF3' strains

Status
Released on 26 August 2014, last updated on 10 December 2014
Organism
Haemophilus influenzae
Samples (12)
Protocols (3)
Description
Nontypeable Haemophilus influenzae (NTHi) is a commensal microorganism of the normal human nasopharyngeal flora, yet also an opportunistic pathogen of the upper and lower respiratory tracts. Changes in gene expression patterns in response to host microenvironments are likely critical for survival. One such system of gene regulation is the ability to carefully regulate iron uptake. A central regulatory system that controls iron uptake, mediated by the ferric uptake regulator Fur, is present in multiple bacteria, including NTHi. Previous work has identified a small RNA, HrrF, that is Fur-regulated in NTHi 86-028NPrpsL.To understand the contribution made by HrrF to gene regulation in NTHi, hrrF was deleted in the NTHi strain 86-028NPrpsL∆fur. Using RNA-Seq, we identified protein-encoding genes whose expression was repressed or activated by HrrF. These data comprise transcriptional anaylses of an rpsL mutant of 86-028NP, an isogenic fur mutant of 86-028NPrpsL, an isogenic fur mutant of 86-028NPrpsL also containing a full deletion of hrrF, and an isogenic fur mutant of 86-028NPrpsL also containing a deletion of only the 3' portion of hrrF. All strains were grown in defined medium containing 10 µg/ml human hemoglobin to mid-log phase. Cells were then harvested and RNA extracted. A total of three biological replicates were generated for these analyses. Analysis of transcriptomes using the Illumina HiSeq 2000 of four strains of nontypeable Haemophilus influenzae which include NTHi 86-028NPrpsL, NTHi 86-028NPrpsL∆fur, NTHi 86-028NPrpsL∆fur∆hrrF, and NTHi 86-028NPrpsL∆fur∆hrrF3' strains. For each strain three biological replicates were analyzed.
Experiment type
RNA-seq of coding RNA 
Contacts
Alistair Harrison <geo@ncbi.nlm.nih.gov>, Estevan A Santana, Robert S Munson Jr
Citation
HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae. Santana EA, Harrison A, Zhang X, Baker BD, Kelly BJ, White P, Liu Y, Munson RS Jr. , PMID:25157846
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-58891.idf.txt
Sample and data relationshipE-GEOD-58891.sdrf.txt
Additional data (1)E-GEOD-58891.additional.1.zip
Links