|
| Status |
Public on Oct 04, 2007 |
| Title |
LmrR Lactococcus lactis MG1363 (slide176536 rep1) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Wild Type
|
| Organism |
Lactococcus cremoris subsp. cremoris MG1363 |
| Characteristics |
Wild Type At OD600=1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA microarray experiments were essentially performed as described (van Hijum et al., 2005;den Hengst et al., 2005c). Briefly, RNA was isolated from two separately grown replicate cultures of L. lactis NZ9000 and the two L. lactis NZ9000 ΔlmrR strains. Strains were grown in GM17 medium and harvested at an OD660 of 1 (late log phase)..
|
| Label |
Cy3
|
| Label protocol |
Subsequently, single-strand reverse transcription (amplification) and indirect labeling of 20 μg of total RNA, with either Cy3 or Cy5 dye, were performed (including a sample in which the dyes were swapped to correct for dye-specific effects). Labeled cDNA samples were hybridized to microarray slides of L. lactis MG1363 spotted in duplicate as described (van Hijum et al., 2005;den Hengst et al., 2005b)
|
| |
|
| Channel 2 |
| Source name |
lmrR mutant
|
| Organism |
Lactococcus cremoris subsp. cremoris MG1363 |
| Characteristics |
Mutant At OD600=1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DNA microarray experiments were essentially performed as described (van Hijum et al., 2005;den Hengst et al., 2005c). Briefly, RNA was isolated from two separately grown replicate cultures of L. lactis NZ9000 and the two L. lactis NZ9000 ΔlmrR strains. Strains were grown in GM17 medium and harvested at an OD660 of 1 (late log phase)..
|
| Label |
Cy5
|
| Label protocol |
Subsequently, single-strand reverse transcription (amplification) and indirect labeling of 20 μg of total RNA, with either Cy3 or Cy5 dye, were performed (including a sample in which the dyes were swapped to correct for dye-specific effects). Labeled cDNA samples were hybridized to microarray slides of L. lactis MG1363 spotted in duplicate as described (van Hijum et al., 2005;den Hengst et al., 2005b)
|
| |
|
| |
| Hybridization protocol |
Hybridization (16 h at 45 °C) of labeled cDNA was performed in Ambion Slidehyb #1 hybridization buffer (Ambion Europe) on superamine glass slides (Array-It; SMMBC), containing technical replicates.
|
| Scan protocol |
Slides were scanned using the Genepix 4200AL DNA micro array slide scanner.
Quantification of the signal of the spots on slides was done with ArrayPro 4.5
|
| Description |
LmrR is a negative transcriptional regulator of the expression of the Multidrug ABC transporter LmrCD in Lactococcus lactis
|
| Data processing |
Slide data were processed and normalized using MicroPreP, and CyberT implementation of the Student's t test (PMID: 15130795).
|
| |
|
| Submission date |
Oct 03, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Anne de Jong |
| E-mail(s) |
[email protected]
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL5048 |
| Series (1) |
| GSE9168 |
LmrR Lactococcus lactis MG1363 |
|
