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| Status |
Public on Feb 12, 2015 |
| Title |
ChIP-seq study of sigma factors in Pseudomonas aeruginosa |
| Organism |
Pseudomonas aeruginosa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Sigma factors are master regulators of bacterial transcription which direct gene expression of specific subsets of genes. In particular, alternative sigma factors are well-known to be key players of bacterial adaptation to changing environments. To elucidate the regulatory network of sigma factors in P. aeruginosa, an integrative approach including ChIP-seq of 11 polyhistidine-tag sigma factors was performed to define the primary regulon of each sigma factor.
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| Overall design |
Sigma factor genes were fused to a polyhistidine-tag and provided in trans. Under optimal conditions regarding sigma factor activity and induction of sigma factor expression, DNA-sigma factor interactions were conserved by formaldehyde treatment. Upon DNA fragmentation by sonication, the complexes were specifically immunoprecipitated by polyclonal anti-6X His-tag antibodies and the purified DNA was analyzed by Illumina sequencing. DNA enrichment to a control strain was calculated and used for peak calling within promoter region (-500,+100) to identify directly regulated genes/operons.
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| Contributor(s) |
Schulz S, Eckweiler D, Häussler S |
| Citation(s) |
25780925, 29738307 |
| |
| Submission date |
Feb 13, 2014 |
| Last update date |
Jul 24, 2019 |
| Contact name |
Denitsa Eckweiler |
| E-mail(s) |
[email protected]
|
| Organization name |
Technische Universität Braunschweig
|
| Department |
Institute of Microbiology
|
| Lab |
Prof. Dieter Jahn
|
| Street address |
Spielmannstr. 7
|
| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
D-38106 |
| Country |
Germany |
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| Platforms (2) |
| GPL18286 |
Illumina Genome Analyzer IIx (Pseudomonas aeruginosa) |
| GPL18287 |
Illumina HiSeq 2500 (Pseudomonas aeruginosa) |
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| Samples (34)
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| This SubSeries is part of SuperSeries: |
| GSE54999 |
Elucidating the Sigmulome of P.aeruginosa PA14 by ChIP-Seq and RNA-Seq approaches |
|
| Relations |
| BioProject |
PRJNA238228 |
| SRA |
SRP037770 |
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