Unknown,Transcriptomics,Genomics,Proteomics

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Early response of potato plants to virus (PVY-NTN) inoculation

ABSTRACT: Potato virus YNTN (PVYNTN), causing potato tuber ring necrosis disease, dramatically lowers the quantity and the quality of the potato yield all over the world. The cultivar Igor is one of the most susceptible cultivars, developing severe disease symptoms on plants as well as on tubers. Finding genes differentially expressed in the early response to infection, when the host response is more defense- than infection- related, could improve our understanding of the potato - PVYNTN interaction. Differential gene expression in early response of potato cv. Igor plants to PVYNTN infection was studied using potato TIGR cDNA-microarrays. Expression was compared between mock inoculated and virus infected plants 12 hours after inoculation, in four biological replicates. Keywords: direct comparison Each microarray was hybridized with a virus inoculated sample and mock inoculated sample from the same biological replicate. Four biological replicates were analyzed.

ORGANISM(S): Solanum tuberosum

SUBMITTER: Ana Rotter 

PROVIDER: E-GEOD-10903 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Finding differentially expressed genes in two-channel DNA microarray datasets: how to increase reliability of data preprocessing.

Rotter Ana A   Hren Matjaz M   Baebler Spela S   Blejec Andrej A   Gruden Kristina K  

Omics : a journal of integrative biology 20080901 3

Due to the great variety of preprocessing tools in two-channel expression microarray data analysis it is difficult to choose the most appropriate one for a given experimental setup. In our study, two independent two-channel inhouse microarray experiments as well as a publicly available dataset were used to investigate the influence of the selection of preprocessing methods (background correction, normalization, and duplicate spots correlation calculation) on the discovery of differentially expre  ...[more]

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