|
| Status |
Public on Oct 01, 2014 |
| Title |
Smutans_42C_10min_rep03 |
| Sample type |
RNA |
| |
|
| Source name |
Smutans, 42C, 10min
|
| Organism |
Streptococcus mutans UA159 |
| Characteristics |
culture temperature: 42℃
heat stress time: 10 minutes
|
| Treatment protocol |
For the heat stress groups, mid-logarithmic phase cell cultures of S. mutans (OD600nm = 0.5) were incubated at 42℃ for 5 min, 10 min, 15 min, 30 min, 45 min and 60 min, respectively.
|
| Growth protocol |
S. mutans strain was routinely grown without shaking in brain heart infusion broth supplemented with 1% sucrose if necessary at 37℃ anaerobically.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immediately after heat stress, all the cell cultures were collected and treated with RNAprotect reagent (Qiagen, Valencia, CA, USA). RNA was extracted and purified using RNeasy Mini kits (Qiagen) and digested with DNase. Purified RNA samples were analyzed by Nanodrop ND 1000 spectrophotometer (Thermo Fisher Scientific, Pittsburgh, PA, USA)
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.
|
| |
|
| Hybridization protocol |
Hybridization was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.
|
| Scan protocol |
Scanning was performed following the standard operating protocol (Agilent). Please see the website http://www.agilent.com/.
|
| Description |
Smutans were cultured in 42C with 10 minutes heat stress, in total of 3 biological repeats, and this is the third one.
|
| Data processing |
The Raw data (txt files) were preprocessed by R/Bioconductor package limma, in which we chose quantile method for normalizaion. For the sibiling probes (multiple probes to one gene), we used the median indensity for representation.
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| |
|
| Submission date |
Jul 10, 2014 |
| Last update date |
Oct 01, 2014 |
| Contact name |
Yulong Niu |
| E-mail(s) |
[email protected]
|
| 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 |
GPL18933 |
| Series (1) |
| GSE59302 |
A time-series transcriptomic changes of Streptococcus mutans in response to heat stress |
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