title: Agilent-021825 3q7q_nov2008
status: Public on Jan 01 2014
contact.city: Pierre Benite
contact.first: Laurent
contact.last: JALLADES
contact.email: laurent.jallades@chu-lyon.fr
contact.address: 165 Chemin du Grand Revoyet
contact.country: France
contact.institute: Hospices Civils de Lyon
contact.phone: 33(0)4 78 86 15 15
organism: Homo sapiens
description: Arrays of this design have barcodes that begin with 16021825 or 2521825.
  
  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.
  
  A custom high-definition oligonucleotide microarray (4x44K, Agilent) was designed for aCGH from the online application tool eArray (version 5.3) and HD-CGH probe library (sequence source UCSC hg18 / NCBI Build 36). This custom microarray combines the capability to scan human genome-wide with an average resolution of approximately 100 Kb and to focus on regions of interest for highest resolution tiling (11 Kb-resolution for either chromosomes 3q and 7q). The array contains about 8,500 and 9,000 oligonucleotides spanning 97 Mb and 105 Mb of the 7q and the 3q chromosomes respectively.
manufacture_protocol: see manufacturer's web site at http://www.agilent.com/