|
| Status |
Public on Oct 01, 2015 |
| Title |
311.1c |
| Sample type |
genomic |
| |
|
| Source name |
swine
|
| Organism |
Yersinia pseudotuberculosis |
| Characteristics |
bioserotype: NA
origin: England
|
| Treatment protocol |
NA
|
| Growth protocol |
Frozen strains were first grown on blood agar under aerobic conditions at 28°C 24 h. To prepare for DNA isolation the strains were grown in TSB-medium at 28°C 24 h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted as described by Pitcher et al. (1989). DNA quality was checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)
|
| Label |
Cy5
|
| Label protocol |
DNA was labeled using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. Labeled DNA was purified with the DNA purification kit (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany). The concentration of DNA and the incorporation of the dye were checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)
|
| |
|
| Hybridization protocol |
Agilent (Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.
|
| Scan protocol |
GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2.
|
| Description |
253640110005_4_2.gpr
|
| Data processing |
Images were processed and checked manually using GenePix Pro 6.0/6.1 software. For data analysis R software LIMMA-package (Smyth et al 2005) was used. Background intensities were fixed using normexp-algorithm (threshold 50).
|
| |
|
| Submission date |
Apr 03, 2015 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Kaisa Aulikki Jaakkola |
| E-mail(s) |
kaisa.jaakkola@gmail.com
|
| Organization name |
University of Helsinki, Faculty of veterinary medicine
|
| Department |
The Department of Food Hygiene and Environmental Health
|
| Street address |
Agnes Sjöbergin katu 2
|
| City |
University of Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
| |
|
| Platform ID |
GPL19993 |
| Series (1) |
| GSE67565 |
Comparative genome hybridization of Enteropathogenic Yersinia |
|
