|
| Status |
Public on Aug 29, 2009 |
| Title |
S10_ swine |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
S10
|
| Organism |
Streptococcus suis |
| Characteristics |
strain: S10
origin: The Netherlands
pathogenicity: Virulent
|
| Growth protocol |
Cells were cultured in Todd-Hewitt broth (THB)(Difco Laboratories, Detroit, MI) medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for Suis test strains and Cy5 for reference strain 05ZYH33) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved,(http://www.nimblegen.com/products/lit/lit.html)
|
| |
|
| Channel 2 |
| Source name |
Reference DNA from 05ZYH33
|
| Organism |
Streptococcus suis |
| Characteristics |
strain: 05ZYH33
pathogenicity: Virulent
|
| Growth protocol |
Cells were cultured in Todd-Hewitt broth (THB)(Difco Laboratories, Detroit, MI) medium.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA was labeled with a Random prime reaction. DNA (1 ug) was mixed with 1 O.D. of 5’-fluorescence dye labeled random nonamer (Cy3 for Suis test strains and Cy5 for reference strain 05ZYH33) (TriLink Biotechnologies) in 62.5 mM Tris-HCl, 6.25 mM MgCl2 and 0.0875% ß-mercaptoethanol, denatured at 98°C for 5 min, chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each in TE) for 2 h at 37°C. Reactions were terminated with 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water. A fifty-fold amplification was typically achieved,(http://www.nimblegen.com/products/lit/lit.html)
|
| |
|
| |
| Hybridization protocol |
Labeled genomic DNA was hybridized to arrays in the NimbleGen Hybridization Buffer for 16 hours at 42oC using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis 05ZYH33 and from each test SS2 strain were co-hybridized to each array. Arrays were washed with NimbleGen wash buffer, and then were spun dry in a microarray high-speed centrifuge (TeleChem International, Inc., Sunnyvale, CA) and stored until scanned.(http://www.nimblegen.com/products/lit/lit.html)
|
| Scan protocol |
Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
|
| Description |
S10_ swine
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.
|
| |
|
| Submission date |
Aug 28, 2009 |
| Last update date |
Aug 28, 2009 |
| Contact name |
Zuo-Wei Wu |
| E-mail(s) |
wuzw@iastate.edu
|
| Organization name |
Iowa state university
|
| Street address |
1113 Veterinary Medicine Bldg
|
| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
| |
|
| Platform ID |
GPL9120 |
| Series (1) |
| GSE17868 |
Mutation Mapping of Streptococcus suis serotype 2 strains |
|
