Microarray Design: FlyChip_long_oligonucleotide_003 (FL003) - INDAC
- Overview
- Materials and Equipment
- Oligo-set documentation
- FL003 probe to transcript mapping
- Meta-grid
- Sub-grid
- 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) and was designed according too the method described in Sykacek et al (2011) BMC Bioinformatics 12:73 (PubMed). 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: GPL14121
How these are printed:
| Probe type | Spots per pin | Spots per array |
|---|---|---|
| Transcript-specific | Between 300 and 312 (randomised) | 14,444 |
| Spike controls | 4 per spike (14 different spikes) | 192 per spike (2,688 for all spikes) |
| Degradation controls | 3 | 144 |
| Spotting buffer | 3 | 144 |
| Not printed | 6 | 288 |
| Empty (additional spotting buffer only) | Between 0 and 12 (randomised) | 532 |
| Total | 380 | 18,240 |
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 65-69mer long oligonucleotide set prepared in conjunction with INDAC
- Gene-specific Arabidopsis thaliana 69mer long oligonucleotide spike controls developed by FlyChip (protocols) and prepared in conjunction with INDAC
- 69mer probe degradation long oligonucleotide set prepared in conjunction with 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_v4.va - tab-delimited FL003 olignucleotide set description, with well locations.
- FL003_v4.gal - Detailed GenePix Array Layout (GAL) FL003 array
- Column definitions - a key for the above files
4. FL003 probe to transcript mapping
These microarray probes were aligned against the transcript fasta sequences of FlyBase release r5.39 (FB2011_07, released July 21st, 2011). Only full length alignments without mismatch against the transcript and genome sequences were considered. The oligo sequence was allowed to extend into the poly-A tail of the mRNA sequence. The following files provide the matched transcript(s) and gene names(s) for each oligo. The detected transcripts within an experiment also depend on the sample preparation and labelling method. The "direct" file (includes direct, indirect and indirect labelling of amino-allyl RNA amplification (protocols)) result in labelled single stranded samples, and these bind only to transcripts in anti-sense orientaion. The "klenow" file (includes klenow and SMART amplification (protocols)) result in labelled double stranded samples which bind to transcripts in anti-sense and sense orientation.
- FL003_direct_transcripts-dmel-r5.39.txt - labelled samples bind to transcripts in anti-sense orientation
- FL003_klenow_transcripts-dmel-r5.39.txt - labelled samples bind to transcripts in anti-sense and sense orientation
- Column definitions - a key to above 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
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Example sub-grid
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7. Spot identities
- MicroGrid II data tracking file formats - a key to each of these file formats.
- Example array picture

