|
| Status |
Public on Jul 01, 2014 |
| Title |
30 min after onset CO2 depletion (2.3) vs CO2 supplemented culture (1.3) 1st of duplicate time series |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
2.3
|
| Organism |
Lactobacillus johnsonii |
| Characteristics |
strain: LA-1
culture condition: 30 min after onset CO2 depletion (2.3)
|
| Treatment protocol |
Cells were harvested at 0.15 OD600 from 50 ml of growth medium by cold centrifugation (5', 2600 * g, 4 C)
|
| Growth protocol |
Cultures were grown in 400 ml batches with MRS at 37˚C under constant pH of 6.5, sparged with gas mixtures 750 ml/min, stirring of ca. 200 rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification
|
| Label |
Cy5
|
| Label protocol |
The Cyscribe Post-labeling kit was used to synthesize cDNA out of 5 µg of total RNA, which was subsequently labeled according to the manufacturer's protocol (Amersham Biosciences, Amersham, Uk).
|
| |
|
| Channel 2 |
| Source name |
1.3
|
| Organism |
Lactobacillus johnsonii |
| Characteristics |
strain: LA-1
culture condition: CO2 supplemented culture (1.3)
|
| Treatment protocol |
Cells were harvested at 0.15 OD600 from 50 ml of growth medium by cold centrifugation (5', 2600 * g, 4 C)
|
| Growth protocol |
Cultures were grown in 400 ml batches with MRS at 37˚C under constant pH of 6.5, sparged with gas mixtures 750 ml/min, stirring of ca. 200 rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by beat-beating and total RNA was isolated by subsequent phenol-chloroform extraction, followed by RNA purification
|
| Label |
Cy3
|
| Label protocol |
The Cyscribe Post-labeling kit was used to synthesize cDNA out of 5 µg of total RNA, which was subsequently labeled according to the manufacturer's protocol (Amersham Biosciences, Amersham, Uk).
|
| |
|
| |
| Hybridization protocol |
To the mixed cDNA's 25 µl Slidehyb #1 hybridization buffer (Ambion, Austin, USA) 2x Hi-RPM hyb. Buffer (Agilent) was added and 40 ul of the resulting solution was applied on the slides
|
| Scan protocol |
Slides were scanned with a ScanArray Express 4000 scanner (Perkin Elmer)
|
| Description |
2.3 over 1.3
1st of duplicate time series
|
| Data processing |
Data were normalized using Lowess normalization as available in MicroPrep and corrected for inter-slide differences. Median intensity of the different probes per gene was selected as the gene expression intensity.
|
| |
|
| Submission date |
Dec 02, 2013 |
| Last update date |
Jul 01, 2014 |
| 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 |
GPL18009 |
| Series (1) |
| GSE52876 |
Genome-wide transcriptome analysis of the oxygen response of L. johnsonii reveals that NADH oxidase is a secondary H2O2 source. |
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