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

Microarray Design: FlyChip004 (FC004) - DGC

1. Overview
2. Materials and Equipment
3. Clone-set documentation
4. Affymetrix to FC004 mapping
5. Meta-grid
6. Sub-grid
7. Spot identities

1. Overview

This microarray format is currently available for use. Each microarray contains 10,080 elements (or 'spots'). This array is composed of DGC release 1 PCR amplicons and some controls. These controls include spikes, i.e., probes complementatary to targets in A. thaliana, spotting buffer, vector markers, and genetic markers. Empty wells in the DGC collection are also printed. The spot layout is randomised to facilitate correction of systematic biases. The spots have an estimated mean diameter of 110 to 130 µm.

How these are printed:

*Empty wells in the DGC set, PCR failures.

2. Materials and Equipment

FC004 microarrays were printed using the BioRobotics MicroGrid II Total Array System and 48 MicroSpot 2500 split-pins on FMB cDNA microscope slides. Probe DNA was dissolved in 150 mM NaPO₄ with 0.01% sarkosyl.

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/)

3. Clone set documentation

The following files provide further information on our clone set. They are currently best viewed in Mozilla (http://www.mozilla.org/). When viewed in Internet Explorer, the column alignment will not be correct.

• FC004.htm - annotated HTML FlyChip004 clone set description. This human readable file is 6,736 kb 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/)
  • FlyBase (http://fly.ebi.ac.uk/)

• FC004.txt - tab-delimited FlyChip004 clone set decription. This machine readable file is 728 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. FC004 to Affymetrix probe-set files

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_FC004.txt - DGC clones and their respective GeneChip® Drosophila Genome Array (DrosGenome1) Affymetrix short oligonucleotide set identities (845 kb)

• cdna2affy2_FC004.txt - DGC clones and their respective GeneChip® Drosophila Genome Array (DrosGenome2) Affymetrix short oligonucleotide set identities (807 kb)

• FC004 to Affymetrix mapping - a brief description of how to make best use of the data in these files

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: 17.55 mm (X-axis) by 53.28 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 15x14 (210) spots, with a centre-to-centre spot distance of 270 µm. The numbers in the layout below refer to 'source visits':

• Source visit '0' - Spot not printed at this location
• Source visit '1 to 14' - Arabidopsis thaliana PCR products (control)
• Source visit '15' - Drosophila vectors and markers (control)
• Source visit '16' - Spotting buffer (control)
• Source visit '17 to 160' - Drosophila Gene collection PCR products
• Source visit '161 to 174' - Arabidopsis thaliana PCR products (control)
• Source visit '175 to 176' - Spotting buffer (control)

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 included)
• FC004.va - FlyChip FC004 array description (1,035 kb)
• FC004.gal - GenePix Array Layout (GAL) FC004 array description (266 kb)