title: VIB Crohn 7k version 2
status: Public on May 03 2007
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 arrray design contains 15,552 features printed in a layout of 12 meta rows and 4 meta columns, consisting out of 18 rows and 18 columns per block.  The array measures the expression of 6,779 features, spotted in duplicate.  Meta column 1 is a replicated in meta column 2 and meta column 3 is replicated in meta column 4.  The Lucidea Universal ScoreCard controls (Amersham Biosciences Buckinghamshire, UK) are added, making a total of 384 controls, also spotted in duplicate (i.e., 768 control spots).  A set of 1,226 spots remained empty.
  The Platform data table reflects a condensed representation of the array. The complete array layout file representing the duplicate-spotted features is linked as a supplementary file.
manufacture_protocol: Equipment:
  1. Generation III microarray spotter (Amersham Biosciences, Buckinghamshire, UK).
  2. 384 microtiter plates (Amersham Biosciences, Buckinghamshire, UK).
  3. UV-crosslinker (Biolink, BLX-254, Vilber Lourmat, France).
  4. Type VII silane coated slides (cat#: RPK0174, Amersham BioSciences, Buckinghamshire, UK).
  Spotting:
  1. Dissolve cDNA array elements in 50% DMSO at concentrations ranging between 100-200ng/µl and array in 20 384 microtiter plates.
  2. Set spotter: normal mode, 69% humidity, 65% inside humidity, spot diameter: 224, spot buffer: 30, and pen deflection:0.508mm.
  3. Make sure room temperature is between 20-24 degrees Celsius.
  4. Place microtiter plates in the plate hotel with A1 in upper right corner.
  5. Place 75 slides on the slide-deck and perform 2 manual pin-washes.
  6. After spotting, let slides dry at 55% humidity for 3 hours and cross-link at 50 mjoules.
  7. Block slides in %SSPE for 30 minutes at room temperature rinse in water and dry in centrifuge.
  8. Slides can be stored for at least 6 months in a dry-cabinet.