• CamSysBiol
• Proteomics
• FlyMine
• FlyBase
• INDAC
• DrosDel
• Affymetrix

Microarray Design: FlyChip002 (FC002)

1. Overview
2. Materials and Equipment
3. Clone-set documentation
4. Affymetrix to FC002 mapping
5. Meta-grid
6. Sub-grid
7. Spot identities

1. Overview

This microarray format is no longer available. Each microarray contained 7,152 printed spots. The spots had an estimated mean spot diameter of between 160 and 180 µm.

2. Materials and Equipment

FC002 microarrays were printed using the BioRobotics MicroGrid II Total Array System contact-printing instrument and 48 BioRobotics MicroSpot 2500 split-pins on in-house coated Poly-L-Lysine glass microscope slides. Probe DNA was dissolved in 150 mM NaPO₄ with 0.01% SDS.

The printed clone-set consisted of:

• Double stranded PCR products generated from the Berkeley Drosophila Genome Project Drosophila Gene Collection (version 1.0) cDNA clones (http://www.fruitfly.org/)

• Double stranded PCR products generated from Arabidopsis thaliana cDNA clones obtained from:
  
  • Arabidopsis Biological Resource Centre (ABRC) (http://aims.cps.msu.edu/)
  • Incyte Genomics (http://www.incyte.com/)
  • Functional Genomics of Plant Stress Tolerance (http://www.stress-genomics.org/)

• Linearised double stranded P element vectors and double stranded PCR products generated from P element vector marker genes obtained from:
  
  • Department of Genetics, University of Cambridge (http://www.gen.cam.ac.uk/)
  • Berkeley Drosophila Genome Project (http://www.fruitfly.org/)

• Cy3 and Cy5 labelled sonicated salmon sperm DNA (protocols)

3. Clone set documentation

The following files provide further information on our clone set. They are currently best viewed in Netscape (http://home.netscape.com/download/). When viewed in Internet Explorer, the column alignment will not be correct.

• FlyChip002.html - annotated HTML FlyChip002 clone set description. This human readable file is 5 Mb in size and will take some time to download. It has links to the following external sites:
  
  • GenBank (http://www.ncbi.nlm.nih.gov/Genbank/)
  • GadFly (http://www.fruitfly.org/annot/)
  • FlyBase (http://fly.ebi.ac.uk/)

• FlyChip002.txt - annotated tab-delimited FlyChip002 clone set decription. This machine readable file is 750 Kb in size and may be viewed in a spreadsheet package such as Excel (Windows) or StarOffice (Unix).

• Column definitions - a key for the above files. Please note that DGC stands for Drosophila Gene Collection

4. Affymetrix to FC002 mapping

These files were made by searching for shared clone identities and/or FlyBase FBgn codes. Please note, there may be more than one Affymetrix short oligonucleotide set identity and/or more than one DCG clone per FlyBase FBgn code. Also, DGC clones that do not have a corresponding Affymetrix short oligonucleotide set identity have been omitted.

• cdna2affy_FlyChip002.txt - DGC clones and their respective GeneChip® Drosophila Genome Array (DrosGenome1) Affymetrix short oligonucleotide set identities

• cdna2affy2_FlyChip002.txt - DGC clones and their respective GeneChip® Drosophila Genome Array (DrosGenome2) Affymetrix short oligonucleotide set identities (coming soon)

5. Meta-grid layout

The meta-grid layout is described below, with the numbers in the layout referring to the pin that printed the sub-grid.

• 4x12 meta-grid
• One meta-grid per slide
• Meta-grid area: 17.22 mm (X-axis) by 53.53 mm (Y-axis)

Meta-grid one

01 02 03 04
05 06 07 08
09 10 11 12
13 14 15 16
17 18 19 20
21 22 23 24
25 26 27 28
29 30 31 32
33 34 35 36
37 38 39 40
41 42 43 44
45 46 47 48

6. Sub-grid layout

Each sub-grid has 12x13 (156) spots, with a centre-to-centre spot distance of 310 µm. The numbers in the layout below refer to 'source visits':

• Source visit '000' - Spot not printed at this location
• Source visit '001 to 144' - Drosophila Gene collection PCR products
• Source visit '145' - PCR products from Arabidopsis thaliana, linearised P element vector, or P element marker gene PCR products
• Source visit '147' - Cy3 and Cy5 labelled sonicated salmon sperm DNA

The sonicated salmon sperm DNA is used to orientate the sub-grids when spot-finding (analysis)

7. Spot identities

• MicroGrid II data tracking file formats - a key to each of these file formats.
• Example sub-grid and spot layout - an example array (warning - large images)