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Status |
Public on Aug 09, 2012 |
Title |
NT77 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
NT77
|
Organism |
Streptococcus suis |
Characteristics |
strain: NT77 serotype: 18 sequence type: ST79 site isolated: Canada origin: healthy pig pathogenicity: unknown sample type: 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 the 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)
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Channel 2 |
Source name |
Reference GZ1 DNA
|
Organism |
Streptococcus suis |
Characteristics |
strain: GZ1 serotype: 2 sequence type: ST1 site isolated: China origin: patient pathogenicity: highly virulent sample type: reference 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 the 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)
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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 GZ1 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)
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Scan protocol |
Arrays were scanned on an Axon 4000B scanner per the manufacturer's protocol.
|
Description |
ICDC_25 Mutation mapping NT77
|
Data processing |
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 CGS data extraction.
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|
Submission date |
Dec 14, 2010 |
Last update date |
Aug 09, 2012 |
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 |
GPL11315 |
Series (1) |
GSE26052 |
Mutation Mapping of 31 Streptococcus suis strains |
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