Microarray Design: FlyChip003 (FC003)
- Overview
- Materials and Equipment
- Clone-set documentation
- Affymetrix to FC003 mapping
- Meta-grid
- Sub-grid
- Spot identities
1. Overview
This microarray format is no longer available. Each microarray contains 7,248 printed spots. This array is composed of 5,849 DGC release 1 PCR amplicon spots. The remainder, 1399 spots, are either additional controls, for example, spotting buffer, vector markers, genetic markers, or they map to empty wells in the DGC collection. The spots have an estimated mean diameter of between 160 and 180 µm.
2. Materials and Equipment
FC003 microarrays were printed using the BioRobotics MicroGrid II Total Array System contact-printing instrument and 48 BioRobotics MicroSpot 2500 split-pins on either FMB cDNA or in-house coated Poly-L-Lysine glass 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/)
- 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.
- FlyChip003.html - annotated HTML FlyChip003 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/)
- FlyChip003.txt - annotated tab-delimited FlyChip003 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. FC003 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_FlyChip003.txt - DGC clones and their respective GeneChip® Drosophila Genome Array (DrosGenome1) Affymetrix short oligonucleotide set identities
- FC003 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: 17.22 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 '146' - PCR products from Arabidopsis thaliana (same clone in every sub-grid)
- Source visit '147' - PCR products from Arabidopsis thaliana, linearised P element vector, spotting buffer, or P element marker gene PCR products
- Source visit '154' - Cy3 and Cy5 labelled sonicated salmon sperm DNA
Sub-grid layout
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Example sub-grid
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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 included)
