Transcriptomics

Dataset Information

5

A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly


ABSTRACT: 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.

ORGANISM(S): Nicotiana benthamiana  

SUBMITTER: Aleksandra Swiercz   Michal Goralski  Paula Sobieszczanska  Marek Figlerowicz  Aleksandra Obrepalska-Steplowska  Agnieszka Zmienko 

PROVIDER: E-GEOD-76631 | ArrayExpress | 2016-01-08

SECONDARY ACCESSION(S): GSE76631PRJNA308198

REPOSITORIES: GEO, ArrayExpress

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