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Functional Genomics for Drosophila
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Microarray Design: FlyChip_long_oligonucleotide_003 (FL003) - INDAC

  1. Overview
  2. Materials and Equipment
  3. Oligo-set documentation
  4. FL003 probe to transcript 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) 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:

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.

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.

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.

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':

Sub-grid layout

Sub-grid layout

Example sub-grid

sub-grid

7. Spot identities