Investigation Title Transcription profiling of two E. coli ABU strains during biofilm growth in human urine Comment[Submitted Name] Hancock V. E. coli Biofilm ABUs Experimental Design co-expression_design strain_or_line_design growth_condition_design transcription profiling by array Experimental Design Term Source REF mo mo mo EFO Comment[ArrayExpressReleaseDate] 2007-02-02 Comment[AEMIAMESCORE] 5 Comment[ArrayExpressAccession] E-MEXP-926 Comment[MAGETAB TimeStamp_Version] 2010-08-11 16:56:01 Last Changed Rev: 13058 Experimental Factor Name strain growth_condition Experimental Factor Type strain_or_line growth_condition Experimental Factor Term Source REF Person Last Name Hancock Roos Klemm Person First Name Viktoria Viktoria Per Person Mid Initials Person Email vro@biocentrum.dtu.dk Person Phone +4545252519 Person Fax Person Address Matematiktorvet Person Affiliation Biocentrum-DTU CBM Biocentrum-DTU Person Roles submitter Person Roles Term Source REF Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2007-02-02 PubMed ID 17145952 Publication DOI 17145952 Publication Author List Viktoria Hancock; Per Klemm Publication Title Global Gene Expression Profiling of Asymptomatic Bacteriuria Escherichia coli during Biofilm Growth in Human Urine Publication Status journal_article Publication Status Term Source REF Experiment Description Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine. Protocol Name P-MEXP-21150 P-MEXP-21149 P-MEXP-36217 P-MEXP-20170 P-AFFY-2 Affymetrix:Protocol:Hybridization-Unknown P-AFFY-6 P-MEXP-36314 Protocol Type grow grow grow nucleic_acid_extraction labeling hybridization feature_extraction bioassay_data_transformation Protocol Description Human urine was collected from four healthy men and women volunteers who had no history of UTI or antibiotic use in the prior two months. The urine was pooled, filter sterilised, stored at 4 degrees and used the following day. Overnight cultures of E. coli 83972 were used for inoculation of 20 ml pooled human urine until reaching exponential phase and then used for inoculation of 50 ml urine to an OD600 of 0.05. 5-ml samples were extracted at mid-exponential phase (OD600 about 0.4) and mixed with 2 volumes of RNAprotect Bacteria Reagent (QIAGEN) to stabilise RNA before purification of RNA using RNeasy Mini Kit (QIAGEN). All cultures were grown at 37 degrees and 130 rpm in a waterbath incubator. Overnight cultures of E. coli 83972 were used for inoculation of 20 ml MOPS-glucose (morpholinopropanesulfonic acid minimal media, supplemented with 0.2% glucose) until reaching exponential phase and then used for inoculation of 50 ml MOPS-glucose to an OD600 of 0.05. 5-ml samples were extracted at mid-exponential phase (OD600 about 0.5) and mixed with 2 volumes of RNAprotect Bacteria Reagent (QIAGEN) to stabilise RNA before purification of RNA using RNeasy Mini Kit (QIAGEN). All cultures were grown at 37 degrees and 130 rpm in a waterbath incubator. Human urine was collected from four healthy men and women volunteers who had no history of UTI or antibiotic use in the prior two months. The urine was pooled, filter sterilised, stored at 4 degrees and used the following day. Freshly grown urine cultures of E. coli were used for inoculation of 25 ml pooled human urine in 94 mm Petri dishes. The cultures were grown statically for 42 h and media was carefully poured off and replaced by fresh preheated media twice during incubation. After incubation the bacterial lawn on each Petri dish was quickly washed twice with 20 ml urine preheated to 37 degrees C and immediately thereafter, 2 ml of a 1 to 2 mixture of PBS and RNAprotectTM Bacteria Reagent (QIAGEN AG) was poured on the lawn of attached cells and incubated for 5 min at room temperature to stabilize RNA. The stabilized mixture was then centrifuged and pellets were stored at -80 degrees C. Purification of total RNA with QIAGEN's RNeasy Protect Mini Kit Title: Affymetrix in vitro transcription. Description: Title: Affymetrix Generic Hybridization. Description: Title: Affymetrix CEL analysis. Description: Transformation of the CEL files was made using dChip (version 1.3+). All files/hybridisations were normalised together and model-based expression index was calculated using PM-only model with default settings. Expression values were then exported to a TXT file. Protocol Parameters max temperature;min temperature; max temperature;min temperature; stop time;start time;max temperature;min temperature; Extracted product;Amplification; Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF mo The MGED Ontology SDRF File E-MEXP-926.sdrf.txt Term Source Name The MGED Ontology ArrayExpress mo EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version