Affymetrix GeneChip E.coli Genome 2.0 Array [E_coli_2]

Global Gene Expression Profiling of the Asymptomatic Bacteriuria Escherichia coli Strain 83972 in the Human Urinary Tract

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

Identification of Genes Important for Growth of Asymptomatic Bacteriuria Escherichia coli in Urine

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Comparison of gene expression profile of E. coli 83972 grown in minimal lab media, in urine and in 3 individual patients.

Growth in media, urine or In vivo

Transcription profiling of E. coli 83972 grown in minimal lab media, in urine and in 3 individual patients

Comparison of gene expression profile of E. coli 83972 grown in minimal lab media, in urine and in 3 individual patients.


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-21151

All patients carried UTI-causing E. coli which were confirmed monocultures and all patients showed significant bacteriuria (>10E8 CFU/ml). Urine samples from the patients were extracted using clean catch technique (mid-stream urine was collected) and a 45-ml sample from each patient was immediately mixed with two volumes of RNAprotect Bacteria Reagent (QIAGEN) and incubated for 5 min at room temperature to stabilise RNA before purification of RNA using RNeasy Mini Kit.

P-MEXP-21469

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/MM difference model with default settings. Expression values were then exported to a TXT file.

Transcription profiling of E. coli 83972 grown in minimal lab media, in urine and in 3 individual patients

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