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Open Access Highly Accessed Research article

Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression

Crystal Sweetman1, Darren CJ Wong1, Christopher M Ford1 and Damian P Drew12*

Author Affiliations

1 Wine Science and Business, School of Agriculture Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia, 5064, Australia

2 Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, 1871, Denmark

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BMC Genomics 2012, 13:691  doi:10.1186/1471-2164-13-691

Published: 11 December 2012

Additional files

Additional file 1:

Absolute expression levels for all NCBI RefSeq transcripts in stages EL 31, 35, 36 and 38 of developing Shiraz grape. Additional file 1 consists of three tables in Microsoft Excel format. Table 1 contains RPKM data for all NCBI RefSeq Vitis vinifera transcripts at developmental stages E-L 31, E-L 35, E-L 36 and E-L 38, and includes their NCBI putative functional annotation, and the closest matching Genoscope accession and Affymetrix Probeset ID for the purpose of cross-referencing to other work. Each Probeset ID is listed once only, and matches to its most similar RefSeq transcript. The cluster to which each gene has been allocated with regards to Figure 3 is also shown. Table 2 contains transcripts expressed with an RPKM of greater than 200 at all four stages of berry development under investigation. Corresponding Genoscope annotations and Affymetrix GeneChip probeset IDs have been assigned through BLASTx and VitisNet Network or Category functional annotations are taken from [32]. Table 3 contains a complete list of all RefSeq transcripts not detected with at least five unique sequencing reads, or with and RPKM ≥ 0.5 in any of the samples.

Format: XLSX Size: 2.9MB Download file

Open Data

Additional file 2:

List of all NCBI RefSeq transcripts specifically up-regulated 3-fold or greater at a single developmental stage, or during veraison. Additional file 2 consists of a Microsoft Excel File containing five worksheets, containing lists of transcripts specifically up-regulated at each developmental stage, or during both veraison stages. RPKM data are also included, as is the NCBI putative functional annotation.

Format: XLSX Size: 3MB Download file

Open Data

Additional file 3:

Primers used for qRT-PCR analysis presented in tabulated format. Microsoft Excel File containing a single worksheet with primer sequences shown for each of 15 genes, including 3 control genes, alongside the gene annotation and accession number.

Format: XLSX Size: 12KB Download file

Open Data