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| Status |
Public on Jun 29, 2015 |
| Title |
Using RNA Seq to define the regulon of the Pseudomonas aeruginosa transcription factor Anr in low-oxygen colony biofilms. |
| Organisms |
Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ∆anr mutants, grown in colony biofilms at 1% oxygen.
Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ∆anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters.
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| Overall design |
mRNA profiles of 12 hour colony biofilms were generated for P. aeruginosa strains PAO1 WT, PAO1 ∆anr, clinical isolate J215, and J215 ∆anr, each in duplicate, by deep sequencing using Illumina HiSeq.
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| Contributor(s) |
Hammond J, Hogan D, Bhuju S |
| Citation(s) |
26078448 |
| |
| Submission date |
May 04, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Deborah A Hogan |
| E-mail(s) |
[email protected]
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Microbiology and Immunology
|
| Street address |
Vail Building Rm 208
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03755 |
| Country |
USA |
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| Platforms (2) |
| GPL18287 |
Illumina HiSeq 2500 (Pseudomonas aeruginosa) |
| GPL18782 |
Illumina HiSeq 2500 (Pseudomonas aeruginosa PAO1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA283002 |
| SRA |
SRP057994 |
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