|
| Status |
Public on May 20, 2014 |
| Title |
NCTC1046 map1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
NCTC1046
|
| Organism |
Streptococcus suis |
| Characteristics |
strain: NCTC1046
serotype: 15
sequence type: ST81
site isolated: Netherland
origin: diseased pig
pathogenicity: virulent
|
| Treatment protocol |
test strain
|
| 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 test strains and Cy5 for reference strain) (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 89/1591 DNA
|
| Organism |
Streptococcus suis |
| Characteristics |
strain: 89/1591
serotype: 2
sequence type: ST25
site isolated: Canada
origin: diseased pig
pathogenicity: virulent
|
| Treatment protocol |
Reference
|
| 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 test strains and Cy5 for reference strain) (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 42 ℃ using a MAUI hybridization system (BioMicro Systems, Inc. Salt Lake City, Utah). Labeled genomic DNA (5ug) from the reference strain Streptococcus suis 89/1591 and from each test 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
|
| Description |
Mutation mapping NCTC1046
|
| Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.
|
| |
|
| Submission date |
Aug 10, 2012 |
| Last update date |
May 20, 2014 |
| Contact name |
Xiao Zheng |
| E-mail(s) |
zhengxiao@icdc.cn
|
| Organization name |
China CDC
|
| Street address |
Liuzi five hao
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL15923 |
| Series (1) |
| GSE40035 |
Mutation Mapping of 40 Streptococcus suis strains |
|
