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Sample GSM1850377 Query DataSets for GSM1850377
Status Public on Dec 24, 2015
Title K3_rep1
Sample type RNA
 
Source name KF147 fermentation 3
Organism Lactococcus lactis subsp. lactis KF147
Characteristics fermentation conditions: 0 mM NaCl, pH 6.5, 27°C, static
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 KF147 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 Cy5
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: 253432310001-1_2: Cy5
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 GPL20801
Series (2)
GSE72043 Transcriptome signatures for robustness of Lactococcus lactis KF147
GSE72045 Transcriptome signatures for robustness of Lactococcus lactis

Supplementary data files not provided
Processed data are available on Series record

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