title: NimbleGen Woodchuck Gene Expression HX3 Microarray
status: Public on Apr 11 2012
contact.city: Nutley
contact.first: Donavan
contact.last: Cheng
contact.email: donavan.cheng@gmail.com
contact.state: NJ
contact.address: 340 Kingsland Ave
contact.department: Translational Research Sciences
contact.country: USA
contact.institute: Hoffmann-LaRoche
organism: Marmota monax
description: After filtering the probe sets by a BLASTN E-value <1e-5 and compression by HomoloGene symbol, 13,448 human homologs were represented on the custom chip. In addition, probe sets which detect WHV polymerase (nt. 258-1750), mature WHsAg (nt. 296-920), WHsAg signal peptide (nt. 2992-3226), WHx (nt. 1503-1887) and WHcAg (nt. 2077-2587) of the WHV7-11 (NC_004107.1) sequence were also included on the chip.
  
  Custom microarray generated from sequences obtained in transcriptome sequencing of woodchuck liver and peripheral blood mononuclear cells (PBMCs).
manufacture_protocol: The Woodchuck Gene Expression Microarray was designed from 48,933 assembled contigs with an average length of 1044 bases, and 12,101 singletons with an average length of 555 bases (total = 61,034). In addition, sequences from 5 different WHV regions (WHV polymerase, mature and signal peptide regions of WHsAg, WHx and WHcAg) were also submitted for chip design, giving a total of 61,039 sequences. Probes were selected based on uniqueness scores and base pairs composition rules and were laid out on a NimbleGen Custom Gene expression HX3 array. The resulting probe set consisted of 58,763 exemplars representing 59,625 final sequences, while we were unable to select probes for 1382 contigs and 32 singletons. The final array design had 12 probes per transcript for 98% of the used sequences, while 2% had between 1 and 11 probes per transcript resulting in a total of 696,666 probes. All the probes were 60 bases long with an average percent GC of 47% and an average Tm of 79.3°C (range 59.9-100.9°C).