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Title: The pilus retraction protein PilT has a global influence on the transcriptome of Neisseria gonorrhoeae      
dateReleased:
09-01-2008
description:
The ATPase protein PilT mediates retraction of type IV pili. We performed microarrays comparing the transcription profile of the Neisseria gonorrhoeae wild-type strain MS11 and its isogenic pilT mutant. 63 open reading frames were found to be differentially regulated in the pilT mutant. Most interestingly, a loss of function mutation in pilT leads to an upregulation of pilE, which encodes the pilus subunit protein. Ngo arrays were generated as custom 8x15 K microarrays (Agilent Technologies) covering all open reading frames (ORFs) from N. gonorrhoeae strain FA1090 (accession number AE004969) supplemented with all ORFs from the gonoccoccal genetic island of strain MS11 (accession number AY803022) by 6 specific 60-mer oligonucleotides per gene on average. Microarray analysis was performed as dual-color hybridization with dye-reversal color-swaps as technical replicates for Cy-dye specific effect compensation and three independent biological replicates. Microarray features were extracted with the FE 9.5.3.1 software from Agilent Technologies using the GE2-v4_95_Feb07 protocol with default settings. Data were loaded into Resolver (Rosetta Biosoftware) using the MAGE-ML loader and analyzed for differential gene expression. Ratio profiles were combined into ratio experiments and regulated genes were identified with a threshold of 1.75 fold-change and anti-correlation of the color-swapped dye reversals, rendering the analysis highly stringent and robust with P values <0.0001 of the results.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-12258
refinement:
raw
alternateIdentifiers:
12258
dateSubmitted:
07-27-2008
keywords:
functional genomics
dateModified:
05-03-2014
availability:
available
types:
gene expression
name:
Neisseria gonorrhoeae
ID:
A-GEOD-7101
name:
Agilent-015957
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12258/E-GEOD-12258.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-12258/E-GEOD-12258.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12258
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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