title: SNU_Breast_CGH_v1.0
status: Public on Jan 17 2008
contact.city: Seoul
contact.first: Wonshik
contact.last: Han
contact.email: hanw@snu.ac.kr
contact.address: 28 Yongon-dong, Chongno-gu
contact.department: Dept. of Surgery
contact.country: South Korea
contact.institute: Seoul National University College of Medicine
contact.phone: 82-2-2072-1958
organism: Homo sapiens
manufacture_protocol: Construction of BAC library
  The array used in this study consists of 4,045 human Bacterial Artificial Chromosomes (BACs), which were spaced approximately 1 Mb on average across the entire genome (MacArrayTM Karyo4000 from Macrogen, Inc., Seoul, Korea). BAC clones were selected from the proprietary BAC library of Macrogen, Inc. Briefly, the pECBAC1 vector was digested with HindIII and size-selected HindIII-digested pooled male DNAs were used to generate a BAC library. These vectors were then transformed into and grown in the Escherichia coli DH10B strain.
  Construction of BAC-mediated array CGH microarray
  All clones were two-end sequenced using an ABI PRISM 3700 DNA Analyzer (Applied Biosystems, Foster City, CA, USA), and their sequences were blasted and mapped according to their positions described in the University of California, Santa Cruz (UCSC) human genome database (http://www.genome.ucsc.edu). Confirmation of locus specificity of the chosen clones was performed by removing multiple loci-binding clones by individual examination under standard fluorescence in situ hybridization (FISH) as described previously. These clones were prepared by the conventional alkaline lysis method to obtain BAC DNA. The DNA was sonicated to generate ~3-kb fragments before mixing with 50% DMSO spotting buffer. The arrays were manufactured by an OmniGrid arrayer (GeneMachine, San Carlos, CA, USA) using a 24-pin format. Each BAC clone was represented on an array as triplicate spots and each array was pre-scanned using a GenePix 4200A scanner (Axon Instruments Inc., Foster City, CA, USA) for proper spot morphology.