title: CGH-SANGER 3K 9
status: Public on May 02 2008
contact.city: Leuven
contact.first: Rekin's
contact.last: Janky
contact.email: Nucleomics.Bioinformatics@vib.be
contact.address: Herestraat 49 Box 816
contact.department: Nucleomics Core
contact.country: Belgium
contact.institute: VIB
organism: Homo sapiens
description: The array contains 3656 distinct BAC and PAC sequences. The bacs were printed in 2 replicates. 3573 BACS are from the Sanger institute. 83 BACS were provided by K.U.Leuven Department CME (Belgium).
  The bacs were amplified by DOP - PCR. In total the array design contains 7744 features printed in a layout of 4 meta rows, 4 meta columns, 22 rows per block and 22 columns per block.
  This grid is printed twice on the glass slides allowing for two microarray assays per slide.
manufacture_protocol: MicroGrid Printing Protocol
  Equipment:
  1. Microgrid (Genomics Solutions, UK).
  2. 384 microtiter plates (X7022, Genetix)
  3. 16 MicroSpot quill pins - 10K (cat# BR001489, Genomics Solutions, UK)
  4. Codelink slides (cat#: 30001100, GE Healthcare).
  Printing 2 arrays of 4x4 blocks on 1 microscope slide:
  1. Dissolve PCR products in 125mM Phosphate buffer, 0.000125% sarcosyl at concentrations ranging between 300 ng/ul and array in 384 microtiter plates.
  2. Set spotter settings for 2 arrays of 4x4 blocks printed with 16 pins: column pitch = 185 um, row pitch = 185 um; Humidity 55%; 61 spots per source visit.
  3. Make sure room temperature is between 20-24 degrees Celsius.
  4. Place microtiter plates in the plate hotel with A1 in front left corner.
  5. Place 60 to 120 slides on the slide-deck.
  6. Start spotting early in the morning and stop spotting procedure at end of the day and remove pin set. Leave spotter overnight with vacuum and humidity settings on. Continue spotting the next morning until all plates are printed.
  7. After spotting, incubate the slides in humid chamber with saturated NaCl for 24 to 72 hours.
  8. Block 1%NH4OH.
  9. Slides can be stored for at least 6 months in a dry-cabinet.