title: MGX_Coffee_microarray_15K [PROBE NAME]
status: Public on Dec 13 2017
contact.city: Montpellier
contact.first: Thierry
contact.last: JOET
contact.email: thierry.joet@ird.fr
contact.address: 911 Avenue Agropolis
contact.department: DIADE
contact.country: France
contact.institute: IRD (Institut de Recherche pour le Développement)
organism: Coffea arabica
description: The Coffea Genome Oligo contains 15.580 70mers representing 15.580 genes.
  The Coffea canephora long oligonucleotide set was designed and synthetized by Operon (Town, State) based on the SGN Coffee built II (15721 unigenes; http://solgenomics.net/ ). An amino linker was attached to the 5'-end of each oligonucleotide. The oligonucleotides, selected to limit secondary structure, have a melting temperature of 67 ± 3°C, length 65 ± 5 bases, GC content 43 ± 5 %. More than 98 % of the oligonucleotides were within 1000 bases from the 3'-end of the available gene sequence. For 195 unigenes, no adequate oligonucleotide could be designed and so correspond to "missing genes". BLAST alignments were performed to identify oligonucleotides that could cross-hybridize with other sequences of the SGN Coffee Built II. Three oligonucleotides (opCocaV10004674, opCocaV10014770, opCocaV10009077) cover more than one unigene. Finally out of 15522 oligonucleotides designed, there are 371 oligonucleotides which have > 70% of overall identity to another unigene and have a contiguous identical length of more than 20nt common to another unigene.
  The set also includes 12 unique positive and 12 unique negative controls provided in 16 replicates in a 384-well plate.
manufacture_protocol: Manufacturing microarrays
  The Coffea Array were spotted using the Amersham Biosciences Lucidea Array spotter on epoxysilane-coated mirror glass slides (Genewave). Negative and positive control oligo were also printed into 24 different sectors of each slide. After printing, the slides were stored at room temperature in a dessicator.