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

Microarray Design: FlyChip_long_oligonucleotide_003 (FL003) - INDAC

1. Overview
2. Materials and Equipment
3. Oligo-set documentation
4. Affymetrix to FL002 mapping
5. Meta-grid
6. Sub-grid
7. Spot identities

1. Overview

This microarray format is currently available for use. Each microarray contains 18,240 elements (or 'spots'). This array is composed of transcript-specific oligonucleotides and controls developed by the International Drosophila Array Consortium (INDAC). These controls include spikes, i.e., probes complementatary to targets in A. thaliana, spotting buffer, and probe degradation. Empty wells in the INDAC set are also printed. The spot layout is randomised to facilitate correction of systematic biases (See, e.g., PubMed). The spots have an estimated mean diameter of 90-120 µm.

This microarray is equivalent to FL002 as it was printed using the same spot layout and a duplicate set of oligos.

Gene Expression Omnibus (GEO) accession: GPL5016

How these are printed:

Further information:

Please refer to the Drosophila Genomics Resource Centre (DGRC) technical report for one experimental comparison of the INDAC long-oligonucleotide set to a PCR amplicon library. Further information about the INDAC oligos is also available from FlyMine.

2. Materials and Equipment

FL003 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 INDAC (INDAC)

• Gene-specific Arabidopsis thaliana 70mer long oligonucleotide spike controls developed by FlyChip (protocols) and prepared in conjunction with INDAC (INDAC)

• 70mer probe degradation long oligonucleotide set prepared in conjunction with INDAC (INDAC)

3. Oligo-set documentation

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

• FL003.txt - tab-delimited FL003 olignucleotide set description, with well locations. This machine readable file is 2,390 kb in size and may be viewed in a spreadsheet package such as Excel (Windows) or StarOffice (Unix).

• FL003.htm - annotated HTML FL003 oligonucleotide set description. This human readable file is 10,389 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://www.flybase.org/)

• Column definitions - a key for the above files

4. FL003 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 FL003 oligonucleotide per FlyBase FBgn code. Also, FL003 oligonucleotides that do not have a corresponding Affymetrix short oligonucleotide set identity have been omitted.

• oligo2affy_FL003.txt - FL003 oligonucleotides and their respective GeneChip® Drosophila Genome Array (DrosGenome1) Affymetrix short oligonucleotide set identities (2,638 kb)

• oligo2affy2_FL003.txt - FL003 oligonucleotides and their respective GeneChip® Drosophila Genome Array (DrosGenome2) Affymetrix short oligonucleotide set identities (2,572 kb)

• FL003 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 19x20 (380) 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 '015' - Drosophila melanogaster probe degradation (control)
• Source visit '016' - Spotting buffer (control)
• Source visit '017 to 328' - Drosophila melanogaster gene-specific long oligonucleotides

Sub-grid layout
Example sub-grid

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)
• FL003.va - FlyChip FL003 array description (3,089 kb)
• FL003.gal - GenePix Array Layout (GAL) FL003 array description (472 kb)
• FL003_long.gal - Detailed GenePix Array Layout (GAL) FL003 array description (2,825 kb)