|
| Status |
Public on Dec 24, 2015 |
| Title |
I1_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
IL1403 fermentation 1
|
| Organism |
Lactococcus lactis subsp. lactis Il1403 |
| Characteristics |
fermentation conditions: 0 mM NaCl, pH 6.0, 27°C, shaken
|
| Treatment protocol |
Harvested cells were resuspended in cold TE buffer with phenol/chloroform, SDS, sodium acetate and zirconia beads, frozen in liquid nitrogen and stored at -80°C.
|
| Growth protocol |
Lactococcus lactis strain IL1403 was grown in chemically defined medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were lysed by bead-beating and total RNA was isolated by subsequent phenol/chloroform extraction.
|
| Label |
Cy3
|
| Label protocol |
5 µg of total RNA was used for cDNA synthesis and indirect labeling with cyanine 5 or cyanine 3
|
| |
|
| Hybridization protocol |
Co-hybridization of Cy5- and Cy3-labeled cDNA probes was performed on these oligonucleotide arrays at 65°C and 10 rpm for 17 h using GEX HI-RPM buffer (Agilent Technologies).
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)
|
| Description |
raw data: 253432110001-1_1: Cy3
|
| Data processing |
The raw expression data were Lowess normalized and scaled to normalized probe expression levels using MicroPreP (van Hijum, 2003). As in general multiple probes were designed for each ORF, the ORF expression level was calculated from the median of its probe signals.
|
| |
|
| Submission date |
Aug 13, 2015 |
| Last update date |
Dec 24, 2015 |
| Contact name |
Annereinou Dijkstra |
| E-mail(s) |
annereinou.dijkstra@nizo.com
|
| Organization name |
NIZO food research
|
| Street address |
Kernhemseweg 2
|
| City |
Ede |
| ZIP/Postal code |
6718 ZB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20800 |
| Series (2) |
| GSE72042 |
Transcriptome signatures for robustness of Lactococcus lactis IL1403 |
| GSE72045 |
Transcriptome signatures for robustness of Lactococcus lactis |
|
