Comment[ArrayExpressAccession]	E-GEOD-52002
MAGE-TAB Version	1.1						
Public Release Date	2014-01-01
Investigation Title	An Ribonuclease T2 Family Protein Modulates Acinetobacter baumannii Abiotic Surface Colonization						
Comment[Submitted Name]	An Ribonuclease T2 Family Protein Modulates Acinetobacter baumannii Abiotic Surface Colonization
Experiment Description	A. baumannii has the propensity to colonize abiotic surfaces and this is thought to mediate its transmission to susceptible patients. We found that disruption of A. baumannii ribonuclease T2 family protein (ATCC 17978 locus A1S_3026) severely diminishes the organism's ability to colonize abiotic surfaces. We used Affymetrix A. baumannii GeneChips (part number PMDACBA1) to compare the gene expression properties of wild type and isogenic ribonuclease T2 family protein mutant cells. A. baumanni strain 98-37-09 (wild type) or isogenic ACJ7 (harboring a EZ-Tn5 insertion in A1S_3026) cells were grown to mid-exponential phase growth in Luria Burtani medium, total bacterial RNA was isolated and subjected to GeneChip hybridization and analysis.  We sought to determine the regulatory effects of A1S_3026.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Dunman	Dunman	Murata				
Person First Name	Paul	Paul	Yoshihiko				
Person Mid Initials		M					
Person Email	paul_dunman@urmc.rochester.edu						
Person Affiliation	University of Rochester						
Person Phone	585-276-5700						
Person Address	Microbiology and Immunology, University of Rochester, 601 Elmwood Avenue, Rochester, NY, USA						
Person Roles	submitter						
Protocol Name	P-GSE52002-1	P-GSE52002-5	P-GSE52002-6	P-GSE52002-2	P-GSE52002-3	P-GSE52002-4	P-GSE52002-7
Protocol Description	The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings. ID_REF =  VALUE = Signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 	cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)	1.5 ug of cDNA were hybrized for 16 hr at 45C on an A. baumannii Affymetrix GeneChip. GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.	Once reaching mid exponential phase 1:1 acetone-ethanol was added to inhibit cellular ribonucleases	Cells were grown to mid-exponential phase (Optical Density 600nm of 0.4-0.5) in LB broth at 37C with aeration (225 rpm in a rotary shaker)	Total bacterial RNA was isolated using Rneasy kits according to the manufacturer's recommendations (Qiagen)	GeneChips were scanned in an Affymetrix 7G GeneArray Scanner
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GENOTYPE						
Experimental Factor Type	genotype						
Comment[SecondaryAccession]	GSE52002						
Comment[GEOReleaseDate]	2014-01-01						
Comment[ArrayExpressSubmissionDate]	2013-11-01						
Comment[GEOLastUpdateDate]	2014-01-02						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-52002.sdrf.txt