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UPSC-BASE –Populus transcriptomics online

  1. Andreas Sjödin1,†,
  2. Max Bylesjö2,†,
  3. Oskar Skogström1,
  4. Daniel Eriksson3,
  5. Peter Nilsson4,
  6. Patrik Rydén5,
  7. Stefan Jansson1,
  8. Jan Karlsson1,*

Article first published online: 8 NOV 2006

DOI: 10.1111/j.1365-313X.2006.02920.x

Issue

The Plant Journal

The Plant Journal

Volume 48, Issue 5, pages 806–817, December 2006

Additional Information

How to Cite

Sjödin, A., Bylesjö, M., Skogström, O., Eriksson, D., Nilsson, P., Rydén, P., Jansson, S. and Karlsson, J. (2006), UPSC-BASE –Populus transcriptomics online. The Plant Journal, 48: 806–817. doi: 10.1111/j.1365-313X.2006.02920.x

Author Information

  1. 1

    Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden,

  2. 2

    Research group for Chemometrics, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden,

  3. 3

    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden,

  4. 4

    Department of Biotechnology, KTH – Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden, and

  5. 5

    Department of Clinical Bacteriology, Umeå University, SE-901 87 Umeå, Sweden

  1. †

    †These authors contributed equally.

* *(fax +46 90 786 6676; e-mail jan.karlsson@plantphys.umu.se).

  1. †

    †These authors contributed equally.

  2. Publication of this paper was delayed until acceptance for publication of ‡.

Publication History

  1. Issue published online: 8 NOV 2006
  2. Article first published online: 8 NOV 2006
  3. Received 24 August 2005; revised 13 December 2005; accepted 21 December 2005.

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Keywords:

  • microarray;
  • database;
  • genomics;
  • expression profiling;
  • transcriptome;
  • bioconductor

Summary

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data. Within UPSC-BASE, researchers can perform standard and advanced microarray analysis procedures in a user-friendly environment. Background corrections, normalizations, quality-control tools, visualizations, hypothesis tests and export tools are provided without requirements for expert-level knowledge. Although the database has been developed primarily for handling Populus DNA microarrays, most of the tools are generic and can be used for other types of microarray. UPSC-BASE is also a repository of Populus microarray information, providing data from 21 experiments on a total of 407 microarray hybridizations in the public domain of the database. There are also an additional 10 experiments containing 347 hybridizations, where the automatically analysed data are searchable.

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