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Sample GSM3770936 Query DataSets for GSM3770936
Status Public on Feb 24, 2020
Title genes expression of SAN2 compared with that of MW2 rep2
Sample type RNA
 
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).
 
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).
 
 
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.
Description Biological replicate 2 of 3. genes expression of SAN2 compared with control MW2.
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.
 
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
 
Platform ID GPL21747
Series (1)
GSE131352 Sa MW2 vs SAN2

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 2.442152154e-001
2 0.000000000e+000
3 0.000000000e+000
4 4.689925534e-003
5 -1.381539398e-002
6 4.289620299e-002
7 -8.233133732e-002
8 3.789181198e-002
9 4.603762615e-003
10 7.795013583e-002
11 1.224673916e-001
12 3.118852256e-002
13 -8.187499301e-002
14 -4.290757340e-002
15 -1.427059593e-001
16 -9.684115885e-002
17 1.907853573e-002
18 -6.671540672e-002
19 4.115300034e-002
20 -1.837404156e-002

Total number of rows: 15643

Table truncated, full table size 348 Kbytes.




Supplementary file Size Download File type/resource
GSM3770936_mmatsuo_US11030397_256409610006_S01_GE2_107_Sep09_1_2.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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