|
| Status |
Public on Apr 21, 2008 |
| Title |
CNET_031 Replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CNET_031 genomic DNA
|
| Organism |
Campylobacter jejuni |
| Characteristics |
Strain CNET_031
|
| Growth protocol |
Cells from each strain were grown as a confluent lawn on Mueller-Hinton agar plates at 42ºC for 36 Hrs. under microaerophilic conditions prior to genomic DNA isolation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 1X10^10 cells were harvested and genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
|
| Label |
Cy3
|
| Label protocol |
Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
|
| |
|
| Channel 2 |
| Source name |
NCTC_11168 genomic DNA
|
| Organism |
Campylobacter jejuni |
| Characteristics |
Strain NCTC_11168
|
| Growth protocol |
Cells from each strain were grown as a confluent lawn on Mueller-Hinton agar plates at 42ºC for 36 Hrs. under microaerophilic conditions prior to genomic DNA isolation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 1X10^10 cells were harvested and genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
|
| Label |
Cy5
|
| Label protocol |
Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
|
| |
|
| |
| Hybridization protocol |
Equivalent amounts of Cy-3 labelled experimental and Cy-5 labelled control genomic DNAs with similar dye incorporation efficiencies were pooled and co-hybridized overnight to the microarray at 37ºC in DIG-easy hyb solution (Roche). Washes performed as described in Taboada et al (2004) J Clin Micro 42:4566-4576.
|
| Scan protocol |
Microarrays were scanned using a Chipreader laser scanner (BioRad, Mississauga, ON) according to the manufacturer’s recommendations. Laser power and gain were adjusted to obtain balanced scans on control spots.
|
| Description |
CGH analysis of Strain CNET_031 vs. Strain NCTC_11168
|
| Data processing |
Features were extracted using ArrayPro Analyzer version 4.5 and imported into the BioArray Software Environment (BASE version 1.2). Spots flagged due to poor spot morphology or low signal intensity (less than 3 X local background) were filtered out. After print-tip Loess normalization, data was used to calculate the average log ratio [log2(Signal Experimental / Signal Control)] of replicate spots
|
| |
|
| Submission date |
Dec 17, 2007 |
| Last update date |
Dec 17, 2007 |
| Contact name |
Eduardo N Taboada |
| E-mail(s) |
eduardo_taboada@phac-aspc.gc.ca
|
| Phone |
+1 (403)-382-5550
|
| Fax |
+1 (403)-381-1202
|
| Organization name |
Public Health Agency of Canada
|
| Lab |
Laboratory for Foodborne Zoonoses
|
| Street address |
PO Box 640, TWP Rd. 9-1
|
| City |
Lethbridge |
| State/province |
Alberta |
| ZIP/Postal code |
T1J 3Z4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL2681 |
| Series (1) |
| GSE9919 |
CGH analysis of Campylobacter jejuni isolates previously analyzed by Multi-Locus Sequence Typing |
|
