|
| Status |
Public on Dec 01, 2010 |
| Title |
Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (wild type vs. LitR mutant) |
| Platform organism |
Aliivibrio salmonicida |
| Sample organism |
Aliivibrio salmonicida LFI1238 |
| Experiment type |
Expression profiling by array
|
| Summary |
Bacterial small RNAs (sRNAs) are trans-encoded regulatory RNAs that typically bind mRNAs by short sequence complementarities and change the expression of the corresponding proteins. Some of the well characterized sRNAs serve critical steps in the regulation of important cellular processes, such as quorum sensing (Qrr), iron homeostasis (RyhB), oxidative stress (OxyS) and carbon metabolism (Spot42). However, many sRNAs remains to be identified, and the functional roles of sRNAs are known for only a small fraction. For example, of the hundreds of candidate sRNAs from members of the bacterial family Vibrionaceae the function is known for only nine. We have in this study significantly contributed to the discovery and verification of new sRNAs in a representative of Vibrioneceae, i.e., the A. salmonicida which causes severe disease in farmed Atlantic salmon and other fishes. A computational search for intergenic non-coding (nc) RNAs in the 4.6 Mb genome identified a total of 233 potential sRNAs and 19 other types of ncRNAs with homologs in Rfam. Depending on a set threshold value our microarray approach identified 50-80 sRNAs that are expressed under different growth conditions, twelve of which were verified by Northern blot analysis. In total our data identify nine previously unrecognized sRNAs.
|
| |
|
| Overall design |
Two-condition experiment, wild type cells (control samples) vs. LitR mutants grown in LB medium (stimulated samples). Samples collected from three different optical densities (OD600nm 0.15, OD600nm 0.5 and OD600nm 0.8). Technical replicates for each sample point: 3 control, 3 stimulated, independently grown and harvested. One replicate per array.
|
| |
|
| Contributor(s) |
Ahmad R, Hansen GA, Hansen H, Hjerde E, Nyrud MJ, Willassen N, Haugen P |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 22, 2010 |
| Last update date |
Mar 23, 2012 |
| Contact name |
Erik Hjerde |
| E-mail(s) |
erik.hjerde@uit.no
|
| Phone |
+47 77646263
|
| Organization name |
University of Tromsø
|
| Department |
Department of chemistry
|
| Street address |
Breivika
|
| City |
Tromsø |
| ZIP/Postal code |
9037 |
| Country |
Norway |
| |
|
| Platforms (1) |
| GPL9985 |
Vibrio salmonicida 5.5K V1.0.1 AROS |
|
| Samples (9)
|
|
| This SubSeries is part of SuperSeries: |
| GSE25558 |
Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida |
|
| Relations |
| BioProject |
PRJNA142439 |
Less...
More...