title: NMC Human 15K duplicate cDNA microarray
status: Public on Feb 03 2006
contact.city: Trondheim
contact.first: Tom 
contact.middle: Even 
contact.last: Wheeler
contact.email: tom.wheeler@ntnu.no
contact.address: Olav Kyrresgt. 3
contact.department: Department of cancer research and molecular medicine
contact.country: Norway
contact.institute: Norwegian University of Science and Technology, NTNU
contact.phone: +47 92228833
organism: Homo sapiens
description: 30000 spots printed with 48 pins:
  12759 genes, of which
  117 with DNR-numbers
  10 spikes, plus 1 "empty", "1 Neg_BC" and 1 "Neg_HS"
  Multippel spots:
  9893 genes are spotted twice
  261 genes are spotted three times
  1745 genes are spotted four times
  1 gene is spotted five times (47359: "endothelin 1")
  1 gene is spotted six times (345935: "MAD (mothers against decapentaplegic, Drosophila) homolog 3")
  13 genes are spotted 48 times (Spikes 1-10, Neg_BC, Neg_HS, " ")
  1 gene is spotted 972 times (empty: "")
manufacture_protocol: The 15k human cDNA duplicate arrays were prepared from a collection of 40k cDNAs purchased from Research Genetics (Huntsville, AL) (see Invitrogen website for the manual: Sequence-Verified cDNA Clones, Catalog nos. 97002.V, 97001.V, 97002.MmV, Version C, February 3, 2003, 25-0627). Plasmids were isolated from overnight bacterial cultures in 96-well plates and cDNA inserts amplified by PCR using M13 primers 5'-ctg caa ggc gat taa gtt ggg taa c and 5'-gtg agc gga taa caa ttt cac aca gga aag a. The PCR products were purified with Montage PCR purification kit (Millipore) and quality and concentration was assessed by agarose gel electrophoresis. The purified PCR products were dissolved in 50% DMSO (about 50-200 ng/ l) and spotted in duplicate onto 25 x 75mm amino-silane coated CMT-GAPS glass slides (Corning, NY) using a MicroGrid II printing robot (BioRobotics; Cambridge, UK). The arrays were spotted with 48 pins and contained 4 x 12 blocks of 25 x 25 spots. The probes were fixed to the slide surface by UV irradiation (200 mJ). The 15k cDNA arrays represent 14018 unique probes, all printed in duplicates. In addition, a few in-house cDNA probes and a set of positive and negative control elements including 10 different PCR products of exogenous DNA from SpotReport™ cDNA Array Validation System (Stratagene, La Jolla, CA) were printed on the arrays. Totally, each array contained 30000 elements including duplicates and controls.