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

Microarray Design: FlyChip_long_oligonucleotide_001 (FL001) - Operon

1. Overview
2. Materials and Equipment
3. Oligo-set documentation
4. Affymetrix to FL001 mapping
5. Meta-grid
6. Sub-grid
7. Spot identities

1. Overview

This microarray format is no longer available. Each microarray contains 21,168 elements (or 'spots'). This array is composed of transcript-specific oligoucleotides and spikes i.e., probes complementatary to targets in A. thaliana, spotting buffer, and housekeeping genes. The spot layout is randomised to facilitate correction of systematic biases. The spots have an estimated mean diameter of between 90 and 120 µm.

How these are printed:

2. Materials and Equipment

FL001 microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO₄.

The printed oligo-set consisted of:

• A gene-specific Drosophila melanogaster 70mer long oligonucleotide set prepared in conjunction with Operon (Operon)

• Gene-specific Arabidopsis thaliana 70mer long oligonucleotide spike controls developed by FlyChip (protocols)

• 70mer random long oligonucleotide set prepared in conjunction with Operon (Operon)

3. Oligo-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.

• FL001.txt - tab-delimited FL001 olignucleotide set description, with spot locations. This machine readable file is 750 Kb in size and may be viewed in a spreadsheet package such as Excel (Windows) or StarOffice (Unix).

• FL001.htm - annotated HTML FL001 oligonucleotide set description. This human readable file is 22 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/)
  • FlyBase (http://www.flybase.org/)

• Column definitions - a key for the above files

• release3-1.fasta - the D. melanogster gene sequences that were used to design the oligonucleotide probes (in FASTA format). This machine readable file is 45,680 Kb in size and may be viewed in a text editor such as WordPad (Windows) or emacs (Unix).

4. FL001 to Affymetrix probe-set files

These files were made by searching for shared FlyBase FBgn codes. Please note, there may be more than one Affymetrix short oligonucleotide set identity and/or more than one FL001 oligonucleotide per FlyBase FBgn code. Also, FL001 oligonucleotides that do not have a corresponding Affymetrix short oligonucleotide set identity have been omitted.

• oligo2affy_FL001.txt - FL001 oligonucleotides and their respective GeneChip® Drosophila Genome Array (DrosGenome1) Affymetrix short oligonucleotide set identities

• oligo2affy2_FL001.txt - FL001 olgionucleotides and their respective GeneChip® Drosophila Genome Array (DrosGenome2) Affymetrix short oligonucleotide set identities

• FL001 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 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 21x21 (441) spots, with a centre-to-centre spot distance of 200 µm. The numbers in the layout below refer to 'pin loadings' or 'source visits':

• Source visit '000' - Spot not printed at this location
• Source visit '001 to 014' - Arabidopsis thaliana gene-specific long oligonucleotides (control)
• Source visit '017 to 328' - Drosophila melanogaster gene-specific long oligonucleotides
• Source visit '329 to 336' - Drosophila melanogaster houskeeping genes, randomly generated long oligonucleotides (control)
• Source visit '340 to 342' - Spotting buffer (control)
• Source visit '345 to 358' - Arabidopsis thaliana gene-specific long oligonucleotides (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)
• FL001.txt - tab-delimited FL001 olignucleotide set description, with spot locations.