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Title: A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly      
dateReleased:
01-08-2016
description:
Gene expression microarray was designed, based on two recently published versions of the N. benthamiana transcriptome (v.3 and v.5). Based on homology searches and hybridization tests we identified the sense strand in 106,684 transcriptome contigs and used this information to design a Nb-105k microarray on Agilent eArray platform. By the hybridization of N. benthamiana roots vs leaves RNA samples we showed high specificity and sensitivity of the new microarray in detection of differentially expressed transcripts. Agilent microarrays in 2x105k format (two microarrays per slide) were used for hybridization of labeled RNA from leaves vs roots of N. benthamiana plants. Four biological replicates were used for two-color design in a dye-swap manner.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-76631
refinement:
raw
alternateIdentifiers:
76631
keywords:
functional genomics
dateModified:
01-17-2016
availability:
available
types:
gene expression
name:
Nicotiana benthamiana
ID:
A-GEOD-21307
name:
Agilent-066813 Nicotiana benthamiana N.bentham_transcriptome_v3
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-76631/E-GEOD-76631.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-76631/E-GEOD-76631.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=GSE76631
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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