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Title: Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 trigger alternative transcriptional host responses      
dateReleased:
06-27-2013
description:
This study analysed the temporal transcriptional response of L. lactis UC509.9 undergoing infection with either Tuc2009 or c2, representing phages of two different species (P335 and c2, respectively) of the family Siphoviridae. For the first time, to our knowledge, both DNA microarrays of the host and high resolution tiling arrays of each phage were used provide corresponding data sets of the entire transcriptome at various points post-infection. DNA microarrays containing oligonucleotide primers representing each of the 2066 annotated genes on the genome of L. lactis UC509.9 (Genbank accession number: CP003157), in addition to complete genome tiling arrays of bacteriophages Tuc2009 NC_002703) and C2 (NC_001706) at 4 bp resolution, were designed using eArray () and ChipD () and obtained from Agilent Technologies (Palo Alto, CA). For sample collection, pre-warmed GM17 (30 °C) was inoculated with 2 % of an overnight culture of L. lactis UC509.9. This was grown at 30 °C under static conditions to an OD600 of 0.13 at which point CaCl2 was added to a final concentration of 10 mM. The culture was further incubated for 10 min to allow equilibration. At this point, the culture was split into two equal volumes. To one, phage (either C2 or Tuc2009) in TBT buffer (100 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2), was added to a final multiplicity of infection (MOI) of 5. To the other, acting as control, a corresponding amount of TBT buffer without phage was added. Samples (60 ml) were collected at 2, 5, 10, 15, 25, 35 and, in the case of Tuc2009 only, 45 min post infection (p.i.) by centrifugation. Pellets were flash frozen in a -80 °C EtOH bath. Samples were then maintained at -80 °C until further processing and analysis.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-45655
refinement:
raw
alternateIdentifiers:
45655
keywords:
functional genomics
dateModified:
06-03-2014
availability:
available
types:
gene expression
name:
Lactococcus lactis subsp. cremoris UC509.9
ID:
A-GEOD-16934
name:
Agilent-032729 (Lactococcus lactis subsp. cremoris UC509.9, Lactococcus phage Tuc2009, Lactococcus phage c2)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-45655/E-GEOD-45655.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-45655/E-GEOD-45655.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45655
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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