|
| Status |
Public on Jan 01, 2010 |
| Title |
Control (no ethanol) vs. Shocked with 8% ethanol for 10 min hyb1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Bacterial culture shocked with 8% ethanol for 10 min, replicate 1
|
| Organism |
Lactiplantibacillus plantarum WCFS1 |
| Characteristics |
strain: WCFS1
|
| Treatment protocol |
Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.
|
| Growth protocol |
For ethanol adapted and control cultures: growth in MRS broth with 8% ethanol or 8% H2O (control) at 20 degrees Celcius until OD600 is 1.0. For ethanol shocked cultures: control cultures harvested at OD600 is 1.0 were shocked for 10 or 30 min with 8% ethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by beat-beating and total RNA was isolated by subsequent fenol extraction
|
| Label |
Cy3
|
| Label protocol |
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| Channel 2 |
| Source name |
Control (no ethanol), replicate 1
|
| Organism |
Lactiplantibacillus plantarum WCFS1 |
| Characteristics |
strain: WCFS1
|
| Treatment protocol |
Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.
|
| Growth protocol |
For ethanol adapted and control cultures: growth in MRS broth with 8% ethanol or 8% H2O (control) at 20 degrees Celcius until OD600 is 1.0. For ethanol shocked cultures: control cultures harvested at OD600 is 1.0 were shocked for 10 or 30 min with 8% ethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by beat-beating and total RNA was isolated by subsequent fenol extraction
|
| Label |
Cy5
|
| Label protocol |
10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label
|
| |
|
| |
| Hybridization protocol |
Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)
|
| Description |
n/a
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. BASE2 plugin used for Lowess normalization. Data not normalized across slides. Normalization across slides performed internally with Cyber T.
|
| |
|
| Submission date |
Aug 27, 2009 |
| Last update date |
Sep 24, 2009 |
| Contact name |
Michiel Wels |
| E-mail(s) |
michiel.wels@nizo.com
|
| Organization name |
NIZO food research
|
| Street address |
Kernhemseweg 2
|
| City |
Ede |
| ZIP/Postal code |
6718 ZB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4318 |
| Series (1) |
| GSE17847 |
Ethanol stress response in Lactobacillus plantarum WCFS1 |
|
