Open Access Highly Accessed Methodology article

Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii

Jörg Toepel1, Stefan P Albaum2, Samuel Arvidsson3, Alexander Goesmann2, Marco la Russa1, Kristin Rogge1 and Olaf Kruse1*

Author Affiliations

1 Algae Biotechnology & Bioenergy, Dept. of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany

2 Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany

3 AG Bioinformatics, GoFORSYS, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany

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BMC Genomics 2011, 12:579  doi:10.1186/1471-2164-12-579

Published: 25 November 2011

Additional files

Additional file 1:

Table S1:Transcript specific sequences for the new Chlamydomonas reinhardtii full genome microarray. Probe identifier, probes sequence and origin for the Chlamydomonas reinhardttii 4*44 K Agilent microarray.

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Additional file 2:

Table S2. Confirmation of the Sequence specificity compared to the newest annotation (Augustus 10.2). Specificity for 60 mer oligonucleotides designed for the Chlamydomonas reinhardttii 4*44 K Agilent microarray with three replicates per transcript model in comparison to AUGUSTUS 10.2 annotation (Description: single: Probe is specific for one specific transcript in the used annotation version, multiple: Probe is not specific to one transcript, but to multiple transcripts in the used annotation version. None: probe is not specific to any transcripts in the used transcriptome version.). A summary for all transcript models with the corresponding specific probes (up to three independent probes per transcript) is given in a second Table.

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Additional file 3:

Table S3. Gene expression of Chlamydomonas reinhardtii under nitrogen starvation. Comparison between RNA-seq [17] (48 h) and microarray data for Chlamydomonas reinhardtii cultures incubated under nitrogen starvation conditions (24 h, 48 h, 72 h, 96 h).

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Additional file 4:

Table S4. Gene expression of Chlamydomonas reinhardtii under sulfur starvation. Comparison between RNA-seq [16] (48 h) and microarray data for Chlamydomonas reinhardtii cultures incubated under sulfur starvation conditions (24 h, 48 h, 72 h, 96 h).

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Additional file 5:

Table S5. Gene expression of Chlamydomonas reinhardtii under nutrient starvation. Transcript levels for genes with differential expression in Chlamydomonas reinhardtii cultures incubated under sulfur and nitrogen starvation conditions (24 h, 48 h, 72 h, 96 h).

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