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Title: Transcription profiling of Methanococcoides burtonii grown at 4 and 23 degrees centigrade to study cold adaptation      
dateReleased:
02-01-2011
description:
Methanococcoides burtonii is member of the Archaea that is a valuable model for studying cold adaptation. We developed a Agilent microarray for determing which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Agilent 8 x 15K custom gene expression microarrays containing 15128 probes were designed based on the M. burtonii genome sequence. The Microarrays were constructed using 60-mer oligonucleotides covering 2236 genes (86.7% of the total number) on the coding strand (10153 oligonucleotides) and the complementary strand (3671 oligonucleotides), and a large number of intergenic regions (707 oligonucleotides) (Table 1). Each gene and intergenic region was covered by 1 to 6 oligonucleotides (average of 4 per gene). Eight independent replicates were performed using competitive hybridization comparing 8 cultures grown at 4°C vs 8 grown at 23°C. Due to the fact that different ORFs have different numbers of oligonucleotides (ranging from one to six) and that experiments were performed in 8 different replicates, each gene (or intergenic region) has 8 – 48 measures of fluorescence.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MEXP-2579
refinement:
raw
dateSubmitted:
02-23-2010
keywords:
functional genomics
dateModified:
06-03-2014
creators:
Stefano Campanaro
availability:
available
types:
gene expression
name:
Methanococcoides burtonii
ID:
A-MEXP-1794
name:
Cavicchioli_Mburtonii_Agilent_15k_v1.0
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MEXP-2579/E-MEXP-2579.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-MEXP-2579/E-MEXP-2579.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
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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