title: MIT-KI zebrafish Zv7+8 15K CGH v1.0
status: Public on Sep 07 2010
contact.city: Cambridge
contact.first: Sebastian
contact.last: Hoersch
contact.state: MA
contact.address: 77 Massachusetts Avenue (E18-366)
contact.department: David H. Koch Institute for Integrative Cancer Research at MIT
contact.country: USA
contact.institute: Massachusetts Institute of Technology
organism: Danio rerio
description: This genomic 15K CGH array was custom designed against zebrafish (Danio rerio) genome assembly danRef5/Zv7 (available at: http://hgdownload.cse.ucsc.edu/goldenPath/danRer5/bigZips/) on the basis of a database of seven million genomic probe sequences provided by Agilent. Probe sequences were later re-mapped with respect to genome assembly danRer6/Zv8 (http://hgdownload.cse.ucsc.edu/goldenPath/danRer6/bigZips/). During this process, probes were annotated with respect to the quality of their mapping to the Zv8 assembly - see table columns 'Zv8:ProbeRemapped' and 'Zv8:ProbeRemappedQualityCode'. The quality code is defined as follows:
  Primary code:
  A: Perfect match over entire probe sequence
  B: Probe sequence matches contiguously with 1 mismatch (BLAT blockCount=1)
  C: Probe sequence matches contiguously with 2-5 mismatches (BLAT blockCount=1)
  X: No match for probe sequence in genomic (Zv8) BLAT results => probe not used under Zv8.
  Z: Best BLAT match worse than per code C => probe not used under Zv8
  Primary code qualifiers (suffixes):
  ' = duplicate matches (quality A,B,C) within under 50K
  ^ = duplicate matches (quality A,B,C) within 50K-250K
  (Longer intervals than 250K between duplicate matches led to rejection => primary code Z)
  + = several matches (4-10), regardless of location and quality
  # = many matches (>10), regardless of location and quality
manufacture_protocol: Agilent (http://www.agilent.com) proprietary.
  http://www.chem.agilent.com/Library/technicaloverviews/Public/5988-8171en.pdf  ("Agilent SurePrint Technology Content centered microarray design enabling speed and flexibility")