title: NimbleGen Populus_reassigned_version_3.0 [poplar_V3]
status: Public on Jun 26 2015
contact.city: Corvallis
contact.first: Glenn
contact.last: Howe
contact.state: OR
contact.address: 321 Richardson Hall
contact.department: Forest Ecosystems and Society
contact.country: USA
contact.institute: Oregon State University
organism: Populus trichocarpa
description: The original microarray was based on v1.1 of the P. trichocarpa genome sequence and aspen cDNAs, and included random GC and other control probes. Each original gene model was represented by two replicates of three different 60mer probes (GEO accession numbers GPL2699 and GPL7424).
  Each probe on the original microarray (GEO accession GPL2699) was reassigned to one gene model from the Populus v3.0 genome assembly.  The new microarray targets 35,048 out of a total of 41,335 Populus v3.0 primary transcripts, with a variable number of 60mer probes per transcript. For probes that could not be assigned to v3.0 transcripts, we retained the original Populus v1.1 gene model or aspen transcript assignment (9,393 gene models).
  We used BLASTN to reassign the probe sequences from GPL2699/GPL7424 to the transcript sequences from the Populus v3.0 genome assembly (file Ptrichocarpa_210_transcript.fa released as part of Phytozome v9.0; http://www.phytozome.net/).  We assigned each array probe to one v3.0 gene model, omitting the filtering of low-complexity probes and using a 75% nucleotide identity cutoff.
  The .ndf and .ngd files are linked below as supplementary files.
  
  designname=poplar_V3
  designid=1876
  
  native array description file:
  2014_12_14_Howe_Populus_V3_60mer.ndf
  2014_12_14_Howe_Populus_V3_60mer.ngd
manufacture_protocol: Proprietary in situ oligonucleotide synthesis. See manufacturer's website at http://www.nimblegen.com/.