Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.

Transcription profiling of two E. coli ABU strains during biofilm growth in human urine

Global Gene Expression Profiling of Asymptomatic Bacteriuria Escherichia coli during Biofilm Growth in Human Urine

Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

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Gene expression profiling of two different E. coli ABU strains during biofilm growth in human urine.


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-20170

Purification of total RNA with QIAGEN's RNeasy Protect Mini Kit

P-MEXP-21149

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. 

P-MEXP-21150

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. 

P-MEXP-36217

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. 

P-MEXP-36314

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.

Transcription profiling of two E. coli ABU strains during biofilm growth in human urine

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