Methodology article
Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species
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* Corresponding author: Massimo Delledonne massimo.delledonne@univr.it
- † Equal contributors
1 Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
2 Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
3 454 Life Sciences, 1 Commercial Street, Branford, CT 06405, USA
BMC Genomics 2009, 10:555 doi:10.1186/1471-2164-10-555
Published: 24 November 2009Additional files
Additional file 1:
Collection date and development stage of berry samples analyzed. Collection date and development stage of berry samples used to constitute the RNA pool analyzed.
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Additional file 2:
Alignment statistics of positive 454 unigene sequences and positive sequences used to design the GrapeArray 1.2. Alignment statistics of 454 unigene sequences with a positive expression call by microarray analysis and sequences used to design the GrapeArray 1.2 with positive call by microarray to known gene loci, unannotated genomic regions and ESTs. Number of gene loci identified, ESTs identified and putative novel genes identified by all sequences mapping to grape genome in the three different libraries considered are given.
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Additional file 3:
Additional Methods. Additional information for the Methods section.
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Additional file 4:
Parameters used for the de novo assembly of single reads with Newbler v1.1 software.
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Additional file 5:
Parameters used for oligo design with OligoArray 2.1.
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