|
| Status |
Public on Aug 31, 2013 |
| Title |
sm_normal_cultured_strains_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
normal cultured strains
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
genotype: Wild type
phenotype: normal
accession: NC_004350
|
| Growth protocol |
For the control group, the S.mutans UA159 strains were cultured in brain heart infusion broth (BHI; Difco, Sparks, MD) at 37℃ in a 5% CO2 atmosphere to mid-logarithmic phase.
For the hyperosmotic stimuli group, the S.mutans UA159 strains were cultured in brain heart infusion broth (BHI; Difco, Sparks, MD) at 37℃ in a 5% CO2 atmosphere to mid-logarithmic phase. Then the strains were submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAProtect Bacteria Reagent (Qiagen) and RNeasy Mini kits (Qiagen). Rnase-Free DNase Set (Qiagen) was used to remove genome DNA. A Nanodrop ND 1000 spectrophotometer (Thermo Scientific) was used to confirm total RNA concentrations, while an Agilent 2100 Bioanalyser (Agilent Technologies, CA, USA) was used to evaluate the RNA quality. The isolated RNA was stored at -80℃ until use.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of S. mutans UA159 cultured in the normal condition. It is the second of three normally cultured biological replicates used in this experiment, each from separate cultures.
|
| Data processing |
The raw data (.pair file) was subjected to RMA algorithm normalization and background correction as implemented in the NimbleScan software package, version 2.6 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 22, 2013 |
| Last update date |
Aug 31, 2013 |
| Contact name |
Yulong Niu |
| E-mail(s) |
yulong.niu@hotmail.com
|
| Organization name |
Max Planck Institute for Plant Breeding Research
|
| Department |
Plant Microbe Interactions
|
| Street address |
Carl-von-Linne-Weg 10
|
| City |
Köln |
| State/province |
Nordrhein-Westfalen |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17184 |
| Series (1) |
| GSE47170 |
Expression analysis of Streptococcus mutans UA159 under Hyperosmotic stress environment |
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