title: NimbleGen Zebrafish 12x135K Array based on Zv9 [090818_Zv7_EXPR]
status: Public on Feb 28 2014
contact.city: Moscow
contact.first: Maia
contact.middle: J
contact.last: Benner
contact.email: maiabenner@gmail.com
contact.state: Idaho
contact.address: 875 Perimeter Drive
contact.department: Biological Sciences
contact.country: USA
contact.institute: University of Idaho
organism: Danio rerio
description: Each probe is replicated 3 times. The design includes random GC and other control probes.
  
  The NimbleGen 12-plex zebrafish microarray 090818_Zv7_EXPR was designed based on the Sanger Zv7 zebrafish genome build. This Platform represents a custom NimbleGen Design File (NDF) that was based on zebrafish genome build (Sanger Zv9). Probe sequences from the NimbleGen microarray (113,549 probes) were aligned to Ensembl Zv9 transcripts (53,067) using the Sequence Search and Alignment by Hashing Algorithm (SSAHA2; parameters -kmer 13, -skip 2, -seeds 2, -score 12, -cmatch 9, -ckmer 6). Alignments were filtered based on the following conditions: (probe length – number of mismatches) ≤ 4, no gapped alignments, common strand per transcript (+/-), probes had only one matching gene, ≥ 3 probes per transcript, and only canonical transcripts (15,650 remaining transcripts).
  
  The Platform data table reflects a condensed representation of the custom NDF's SEQ_ID features.
manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.