title: Agilent-023844_Dreissena_IDAEA_15k
status: Public on Jan 22 2012
contact.city: Barcelona
contact.first: Anna
contact.last: Navarro Cuenca
contact.email: anna.navarro@dpi.nsw.gov.au
contact.state: Barcelona
contact.address: C/Jordi Girona 18-26
contact.department: Environmental Toxicology
contact.country: Spain
contact.institute: IDAEA-CSIC
organism: Dreissena polymorpha
description: Arrays of this design have barcodes that begin with 16023844 or 2523844.
  Orientation:
  Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
  The ID column represents the Agilent Feature Extraction feature number.
  Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).
  To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.
manufacture_protocol: The array for Dreissena polymorpha was designed using the eArray tool from Agilent (https://erray.chem.agilent.com/erray/).
  A total of 4057 sequences were compiled from the GeneBank using the EBI website (European Bioinformatic Institute, http://srs.ebi.ac.uk).
  From these sequences, 3253 belongs to Dreissena rostriforme, 705 to D. polymorpha and the rest to other bivalve species.
  An 8x15 Array (a slide with 8 arrays with 15000 probes) was designed using primers of 60 nucleotides.
  Three probes for each sequence were designed following a position criteria zone (5’, center, and 3’), using the eArray software from Agilent.
  Three extra probes were also designed from each gene, based in the criteria of non self-complementation and low redundancy. After eliminating redundant probes, the array included from four to six probes for each gene sequenced