Dataset features


Application: Gene expression microarray analysis
Number of samples: 4
Release date: Feb 27 2009
Last update date: Mar 20 2012
Access: Public
Diseases: Uterine Cervicitis, Gonorrhea, Infection
Chemicals: Nitric Oxide
Dataset link Transcriptional Profiling of Neisseria gonorrhoeae biofilm

Experimental Protocol

Six biofilm flow chambers were inoculated with N. gonorrhoeae strain 1291 wildype. Flow chambers were inoculated with approximately 1 ml of a cell suspension (in biofilm media) from an overnight plate that was suspended to an OD600 of 0.3. Two flow cells each were supplied by a single reservoir of media and the runoff from these two flow cells was passed through a sterile glass wool filter for the removal of detached biofilm flocs, and collected in a sterile waste flask and cultured to assess culture purity. At this time, the waste flask was replaced with a second sterile flask containing 10 ml of RNAlater® (Qiagen Corporation, Valencia, CA) and 100 µl of 10% sodium azide. For the final 24 hours of biofilm growth, the filtered planktonic effluent was collected in this solution to preserve the RNA and prevent transcriptional changes from occurring. Planktonic RNA was extracted from the collected effluent of the two flow cells, while each biofilm RNA was extracted directly from these two flow cells. RNA purity was assessed on an Agilent 2100 Bioanalyzer (Quantum Analytics, Foster City, CA), and only samples with RNA integrity numbers of 7.5 or greater were used for hybridization to microarrays. All six samples had RNA integrity numbers of 7.5 or greater. Therefore, we elected to hybridize the two samples with the highest integrity numbers.








Megan Falsetta