|
| Status |
Public on Dec 05, 2006 |
| Title |
Comparative genomic hybridisation of E. coli WK8 (experiment 1) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
reference strain
|
| Organism |
Escherichia coli |
| Characteristics |
labelled chromosomal DNA of the laboratory strain K-12 MG1655
|
| Biomaterial provider |
A. Postma, The Netherlands
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from an LB overnight culture with genomic DNA purification kit (Fermentas GmbH, Germany) according to the manufacturers instructions.
|
| Label |
Cy3-dCTP
|
| Label protocol |
random hexamer-primed labelling according to the protocol of DeRisi (www.microarrays.org/pdfs/GenomicDNALabel_A.pdf)
|
| |
|
| Channel 2 |
| Source name |
WK8_1
|
| Organism |
Escherichia coli |
| Characteristics |
environmental strain WK8
isolated from source water in the Limmat valley, Switzerland
ECOR group A
biological replicate No. 1 (Cryoculture streaked out, single colony inoculated in LB tube)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from an LB overnight culture with genomic DNA purification kit (Fermentas GmbH, Germany) according to the manufacturers instructions.
|
| Label |
Cy5-dCTP
|
| Label protocol |
random hexamer-primed labelling according to the protocol of DeRisi (www.microarrays.org/pdfs/GenomicDNALabel_A.pdf)
|
| |
|
| |
| Hybridization protocol |
Overnight incubation in sealed boxes in water bath at 42°C.
3 washing steps
Procedure as described in the manufacturers protocol (MWG)
|
| Scan protocol |
Affimetrix 428 scanner, standard scan protocol for microarray glass slides, appropriate adjustion of gain
|
| Description |
Goal of the study was to analyse the prevalence of MG1655 genes in environmental Escherichia coli. The strains were isolated during routine screening of drinking water catchment sites in Switzerland
|
| Data processing |
manual control and correction of spot quantification areas, normalisation of total Cy5 intensity to total Cy3 intensity
|
| |
|
| Submission date |
Nov 30, 2006 |
| Last update date |
Dec 04, 2006 |
| Contact name |
Julian Ihssen |
| Organization name |
EMPA
|
| Street address |
Lerchenfeldstrasse 5
|
| City |
St. Gallen |
| ZIP/Postal code |
9014 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL534 |
| Series (1) |
| GSE6407 |
Comparative genomic hybridization of environmental Escherichia coli isolates indicates highly conserved ecophysiology |
|
