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Status |
Public on Feb 24, 2020 |
Title |
genes expression of SAN2 compared with that of MW2 rep1 |
Sample type |
RNA |
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Channel 1 |
Source name |
MW2
|
Organism |
Staphylococcus aureus |
Characteristics |
treatment: control (unexposed)
|
Growth protocol |
S. aureus MW2 and SAN2 strains were grown in TSB at 37֠°C with shaking. When bacterial OD660 reached 0.4, bacterial cells were collected by centrifugation at 5000xg for 5 min at 4֠°C.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted using acid phenol following manufacturer's instructions
|
Label |
Cy3
|
Label protocol |
10 µg of total RNA were primed with 1 µl of 500 µM random primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of AffinityScript HC RTase (Stratagene), and dNTP mix with amino allyl dUTP. 5 µl of the cDNA was mixed with 5 µl of Cy3 or Cy5 for 30 min. The labeled cDNA was purified using nicleotide purification kit (Qiagen).
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Channel 2 |
Source name |
SAN2
|
Organism |
Staphylococcus aureus |
Characteristics |
treatment: nisin high resistant strain derived from MW2
|
Growth protocol |
S. aureus MW2 and SAN2 strains were grown in TSB at 37֠°C with shaking. When bacterial OD660 reached 0.4, bacterial cells were collected by centrifugation at 5000xg for 5 min at 4֠°C.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA extracted using acid phenol following manufacturer's instructions
|
Label |
Cy5
|
Label protocol |
10 µg of total RNA were primed with 1 µl of 500 µM random primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of AffinityScript HC RTase (Stratagene), and dNTP mix with amino allyl dUTP. 5 µl of the cDNA was mixed with 5 µl of Cy3 or Cy5 for 30 min. The labeled cDNA was purified using nicleotide purification kit (Qiagen).
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Hybridization protocol |
GE hybribuffer HIRPM and GE Bloking solution (Roche) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
Scan protocol |
Scanned on an Agilent scanner.
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Description |
Biological replicate 1 of 3. genes expression of SAN2 compared with control MW2.
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Data processing |
Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1). Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.
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Submission date |
May 16, 2019 |
Last update date |
Feb 26, 2020 |
Contact name |
Miki Kawada-Matsuo |
E-mail(s) |
mmatsuo@dent.kagoshima-u.ac.jp
|
Phone |
81-99-275-6152
|
Organization name |
Kagoshima University
|
Department |
Graduate school of medical and dental sciences
|
Lab |
oral microbiology
|
Street address |
8-35-1, Sakuragaoka
|
City |
Kagoshima |
ZIP/Postal code |
8908544 |
Country |
Japan |
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Platform ID |
GPL21747 |
Series (1) |
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