Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening

doi:10.1186/1471-2164-9-176

BMC Genomics

Volume 9

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Moschella A
Beretta O
Vitulli F
Ranalli P
Perata P

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Vitulli F
Ranalli P
Perata P
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Research article

Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening

Paolo Bagnaresi¹ , Anna Moschella² , Ottavio Beretta³ , Federico Vitulli³ , Paolo Ranalli⁴ and Pierdomenico Perata⁵

¹CRA-GPG, Genomic Research Center, Via S. Protaso 302, I-29017 Fiorenzuola d'Arda (PC), Italy

²CRA-CIN, Research Center for Industrial Crops, 40128 Bologna, Italy

³Genopolis, Department of Biotechnology and Bioscience, University of Milano-Bicocca, 20126 Milan, Italy

⁴CRA-DTI, Department of Processing and Technology Development of Agricultural Products, Roma, Italy

⁵Plant and Crop Physiology Laboratory, Scuola Superiore Sant'Anna, 56127 Pisa, Italy

author email corresponding author email

BMC Genomics 2008, 9:176doi:10.1186/1471-2164-9-176


Published:	16 April 2008

Additional files

Additional file 1:

Tomato-Potato Global Match File part 1 (GMF 1). All GeneChip tomato target sequences were blasted against TIGR potato TA (release 2). Matches below a 5% perfect alignment threshold were discarded. The alignments are listed in separate sheets due to size constraints and are split into five parts (part 1 to 5). Parts 1 and 2 are contained in this first file (GMF 1), and parts 3 to 5 are included in additional file 2 (GMF 2). The first part of the Global Match File also includes alignments scoring above the 90% and 70%_PERF_ALIGN thresholds (ALL_90% and ALL_70% sheets, respectively). As a single probeset can produce more than one hit, both > 90% and > 70% sheets are accompanied by a further sheet listing non-redundant probesets above the corresponding threshold. The Global Match File was split into two parts due to upload size limits. Ideally the two files should be merged back together, this would then enable searches to be performed with just one query across the whole Global Match File alignments

Format: RAR Size: 6.9MB Download file

Additional file 2:

Tomato-Potato Global Match File part 2 (GMF 2). Global Match File parts 3 to 5; see additional file 1.

Format: RAR Size: 6.9MB Download file

Additional file 3:

differentially expressed genes (DEG) list. DEG are sorted in order of decreasing fold induction (expressed as Log fold changes). Each tomato probeset is accompanied by the three best matching potato TA sorted in order of decreasing alignment (%_PERF_ALIGN). For each TA, perfect alignment values, TA identification number and TA annotation are reported. Fields are separated by the "-|-" string.

Format: XLS Size: 939KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 4:

List of primers and TaqMan probes used in qPCR analysis. Sequences of Gene-specific primers and TaqMan probes used for qPCR experiments are reported.

Format: DOC Size: 66KB Download file

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