title: Phytophthora parasitica array
status: Public on Mar 01 2014
contact.city: Sophia Antipolis
contact.first: Gourgues
contact.last: Mathieu
contact.email: mathieu.gourgues@sophia.inra.fr
contact.address: 400 routes des Chappes, BP167
contact.department: UMR Institut Sophia Agrobiotech
contact.country: France
contact.institute: University of Nice Sophia Antipolis
organism: Phytophthora nicotianae
description: The platform was obtained using contig sequences derived from the Phytophthora parasitica EST sequences available in public databases. The EST were obtained from various developmental stages including cell types involved in plant infection. A total of 12632 ESTs was assembled in 1572 contigs and 3879 singletons giving a final 5451-unisequence set. We ascribed 4398 sequences (81 %) to Phytophthora parasitica and 729 sequences (13 %) to plant. The origin of 324 sequences (6 %) remained unknown.    DESIGN_ID DESIGN_NAME DESCRIPTION   7680 080529_Phytophthora_parasitica_expr expression design for Phytophthora parasitica; customer provided 5451 seqs + 11 control seqs; 11 probes/seq, used full transcript length,  pos_weight=50, removed grossly overlapping probes by hand (56,524 probes, 5438 exemplars for 5438 seqs, 1217 seqs had fewer than 11 probes, 24 seqs with no probes); 4 cy of each probe on array
  The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are linked below as supplementary files.
manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.