title: Agilent-022085 SIMR Nematostella 44k 11-2008 [Agilent feature number version]
status: Public on May 01 2013
contact.city: Kansas City
contact.first: Chris
contact.middle: W
contact.last: Seidel
contact.email: seidel@phageT4.org
contact.state: MO
contact.address: 1000 E 50th St
contact.department: Genomics
contact.country: USA
contact.institute: Stowers Institute
contact.phone: 816 926 9054
organism: Nematostella vectensis
description: The array was designed by Chris Seidel in October of 2008 and comprised a 43,803 60-mer probe set targeting 43,787 sequences consisting of 20,456 JGI predictions and EST clusters, 16,816 StellaBase predictions, and 6,515 UniGene predictions, EST clusters, and mRNAs. Design targets from each source were evaluated for redundancy by BLAST, and probes were picked to represent the broadest representation of genes across sources. For nearly identical design targets from different sources, one probe was chosen to represent both. As such, probes may be named based on a source, but may also represent a sequence from another source. The digits forming the suffix of each probe name reflect the distance between the probe and the 3' end of the target gene model. This probe set was submitted to Agilent for their 4x44k platform under design ID: 022085.
  
  Arrays of this design have barcodes that begin with 16022085 or 2522085.
  
  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: see manufacturer's web site at http://www.agilent.com/