The halibut microarrays has been designed based on EST information from Atlantic halibut acquired as part of the Pleurogene project as well as 890 publicly available ESTS available from GenBank. The microarray contains 50-mer oligos representing 9625 different ESTs as well as controls containing an Arabidopsis coding sequence and those containing only buffer. Oligos are spotted as side-by-side quadruplicates on Schott Nexterion E glass slides, giving a total of 39936 spots. Oligonucleotide design, synthesis and spotting was done at the Atlantic Cancer Research Institute in Moncton, New Brunswick. Microarray experiments involving Atlantic halibut are conducted and analysed at the IMB Microarray Facility. View an example experiment result here.
The Senegal sole microarray contains 4,550 different 60mer oligos based on sole ESTs, as well as 320 oligos for the detection of potential miRNAs (designed from zebrafish sequences available in public databases) and 216 oligos based on the most conserved regions between halibut and sole. These oligos are synthesized in situ by Agilent. Microarray experiments involving Senegal sole will be conducted and analysed at Oryzon Genomics in Barcelona.
High-quality total RNAs (RIN >9) are labeled using the Invitrogen Direct Labelling Kit with fluorescent Alexa dyes and the control and experimental samples are co-hybridised to the slide.
Layout of four subgrids (of 48 total) of halibut microarray. Arabidopsis controls are the 16 (12 in rightmost subgrid) spots on the bottom row of each subgrid. Oligos are spotted as side-by-side quadruplicates.
