|
| Status |
Public on Jan 01, 2010 |
| Title |
WCFS1_cggR+ (rib) vs cggRKO (rib) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
cggR+
|
| Organism |
Lactiplantibacillus plantarum WCFS1 |
| Characteristics |
strain: WCFS1
genotype: pSIP409/cggR-P25
strain duplicate (a or b): A
carbon source: Ribose
|
| Treatment protocol |
Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.
|
| Growth protocol |
A defined medium for lactobacilli (DML) (36; Møretrø et al 1998) was used in the growth experiments, with the following modification: The succinate buffer was replaced with 0.1 M MES buffer, and 12 mM glucose or 12 mM ribose was used as carbon source. Gro
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from exponentially growing L. plantarum strains (OD600 of 0.65) using the RNeasy Protect Bacteria Mini Prep Kit (Qiagen). Samples (3 ml) were collected and added to RNA Protect Bacteria Reagent (Qiagen) (6 ml), vortexed for 5 s, in
|
| 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 |
cggRKO
|
| Organism |
Lactiplantibacillus plantarum WCFS1 |
| Characteristics |
strain duplicate (a or b): A
strain: WCFS1
genotype: cggR-mutant
carbon source: Ribose
|
| Treatment protocol |
Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.
|
| Growth protocol |
A defined medium for lactobacilli (DML) (36; Møretrø et al 1998) was used in the growth experiments, with the following modification: The succinate buffer was replaced with 0.1 M MES buffer, and 12 mM glucose or 12 mM ribose was used as carbon source. Gro
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from exponentially growing L. plantarum strains (OD600 of 0.65) using the RNeasy Protect Bacteria Mini Prep Kit (Qiagen). Samples (3 ml) were collected and added to RNA Protect Bacteria Reagent (Qiagen) (6 ml), vortexed for 5 s, in
|
| 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 |
cggR+ (rib) vs cggRKO (rib)
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used
|
| |
|
| Submission date |
Oct 06, 2009 |
| Last update date |
Oct 07, 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) |
| GSE18435 |
Analysis of the role of CggR in Lactobacillus plantarum NC8 and WCFS1 by transcriptome analysis |
|
