http://ag.arizona.edu/microarray/Web2.gif

Arabidopsis Oligonucleotide Microarrays Version 3.0



 

Deconvolving the microarrays:

The print format comprises a single array printed using 48 pins.  The array contains 12 metarows and 4 metacolumns, with the subarrays containing 25 columns and 26 rows with a spacing of 170 x 165 microns.  The dimensions of typical microarrays are given here (Powerpoint file).  Red Reflectance and Syto-61 Stained and/or hybridization images are provided below.

The deconvolution files linking array elements with corresponding gene identifiers are provided below as Excel files, GenePix Array List files (GAL), and/or text files.  Please check the numbers printed on the slide labels, and download the decode file that corresponds to those numbers.

For a discussion of QC aspects of deconvolution, please follow this link.

On all microarrays, we include array elements comprising the Stratagene SpotReportTM Oligo Array Validation System.  This permits use of external normalization methods. The element locations are listed in the deconvolution files. 

Complete array element sequence information is available from Operon at the following link:  http://omad.operon.com/download/index.php

Slide Numbering Scheme

http://ag.arizona.edu/microarray/Microarrayformat3-0.jpg

The microarrays are coded according to the following scheme:

XX refers to the lot number of the oligonucleotides used for printing. YY refers to the print run number, and ZZZ refers to the slide number within the print run (from 1-308).

These numbers allow us to track individual slides for QC purposes.


 

Microarray Designation

Reflectance Image

Syto-61 Image

Hybridization

Image (9-mers)

 Hybridization Image (cRNA)

Deconvolution

Files

GEO Platform

Notes

AT v3 01.01.Z

Array 100

Array 100

Excel

GAL

GPL1787

AT v3 01.02.Z

Array 146

Array 146

Excel

GAL

GPL1788

AT v3 01.03.Z

Array 093

Array 093

TXT

GAL

GPL1775

AT v3 01.04.Z

Array 093


Array 093

Excel

GAL

GPL1775

AT v3 02.01.Z

Array 030

Array 030

TXT1*

TXT2

GAL1*

GAL2

GPL1941

AT v3 02.02.Z

Arrays 246, 290

TXT1

TXT2

 GAL1

GAL2

GPL2508

AT v3 02.03.Z

Arrays 140, 260

Arrays 198, 200, 212, 276 

GAL1

GAL2

GPL2508

AT v3 02.04.Z

Array 251

GAL1

GAL2

GPL2508

AT v3 03.01.Z

Array 137

Array 137

GAL1

GAL2

GPL2508

1

AT v3 03.02.Z

Array 103

 

Array 103

 

TXT1

TXT2

GAL1

GAL2

GPL3006

 

AT v3 03.03.Z

Array 138

Array 138

TXT1

TXT2

GAL1

GAL2

GPL3281

AT v3 04.01.Z

 

 

Array 20, Array 40

 

TXT1

TXT2

GAL1

GAL2

GPL3512

 

AT v3 04.02.Z

 

 

Array 20, Array 40

 

TXT1

TXT2

GAL1

GAL2

GPL3513

 

AT v3 04.03.Z

Array 1

 

Array 1

 

TXT1

TXT2

GAL1

GAL2

GPL3702

 

AT v3 04.04.Z

 

 

Array 40

 

TXT1

TXT2

GAL1

GAL2

GPL3702

 

AT v3 05.01.Z

Array 20

 

Array 20

Array 184

TXT1

TXT2

GAL1

GAL2

GPL3702

 

AT v3 05.02.Z

Array 20

 

Array 20

 

TXT1

TXT2

GAL1

GAL2

GPL4570

 

AT v3 05.03.Z

Array 262

 

Array 262

 

TXT1

TXT2

GAL1

GAL2

GPL4570

 

AT v3 06.01.Z

Array 257

 

Array 258

 

TXT1

TXT2

GAL1

GAL2

GPL4570

 

AT q3 06.02.Z

Array 232

 

Array 232

 

TXT

 

GAL

 

GPL7092

2

AT q3 06.03.Z

Array 105

 

Array 105

 

TXT

 

GAL

 

GPL5827

2

AT q3 06.04.Z

Array 189

Array 189

TXT

GAL

GPL7092

2

AT q3 07.01.Z

Array 396

 

Array 398

 

TXT

 

GAL

 

GPL7092

2

AT q3 07.02.Z

Array 349

Array 349

TXT

GAL

GPL7092

2

AT q3 07.03.Z

Array 267

Array 267

TXT

GAL

GPL7092

2

AT q3 07.04.Z

Array 012

Array 135

TXT

GAL

GPL7725

AT q3 08.01.Z

Array 191

Array 191

TXT

GAL

GPL7092

AT q3 08.02.Z

Array 247

Array 248

TXT

GAL

GPL4570

AT q3 08.03.Z

3

AT q3 08.04.Z

Array 261

Array 261

TXT

GAL

GPL7092

AT3.9.1.Z

Array 029

Array 029

TXT

GAL

GPL4570




*TXT1, TXT2, GAL1 and GAL2 files provide Operon ID numbers and At locus numbers respectively (note: these files were updated on September 23, 2005).
2TXT and GAL files updated November 6, 2008.

3Used for QC purposes.

Questions, comments, or suspected problems should be communicated to: David Galbraith
Page last updated June 9, 2010