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

Arabidopsis Oligonucleotide Microarrays Version 1.0


 

Deconvolving the microarrays:

The initial format (Print Format 1) involved two large arrays which were printed sequentially: Array 1 was printed using 32 pins, and comprises 27 x 27 subarrays.  Array 2 was printed using 8 pins and comprises 27 x 18 subarrays (Powerpoint file).   This format provides 27,216 available element addresses, not all of which were employed for printing.

Print Format 2 (which is used currently) involves one array printed using 48 pins.  It comprises 12 metarows and 4 metacolumns, and the subarrays comprise 24 columns and 25 rows.  The dimensions of typical microarrays are given here (Powerpoint file).

The deconvolution files linking array elements with corresponding gene identifiers are now routinely provided below as Excel files (*.xls).  Other formats (text files (*.txt), GenePix Array List files (*.gal)) are available on request.  Wherever possible, the name of the microarray print run is included in the file header as a cross-check.

For an Excel file linking identifier to At locus number and sequence, please follow this link.

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

 

ORIGINAL

*ENHANCED

GEO Platform

Microarrays AtOligo 1.2.1.Y

Array 1 (.txt)

Array 1 (.xls)

     

 

Array 2 (.txt)

Array 2 (.xls)

 

Microarrays AtOligo 1.3.1.Y

Array 1 (.txt)

Array 1 (.xls)

 

Array 2 (.txt)

Array 2 (.xls)

 

Microarrays AtOligo 1.4.1.Y

Array 1 (.xls)

Array 1 (.xls)

 

Array 2 (.xls)

Array 2 (.xls)

 

Microarrays AtOligo 1.6.1.Y

Array 1 (.txt)

Array 1 (*.gal format)

Array 1 (.xls)

 

Array 2 (.txt)

Array 2 (.gal)

Array 2 (.xls)

 

Microarrays AtOligo 1.7.1.Y

Array 1 (.xls)

Array 1 (.xls)

Comments

 

Array 2 (.xls)

Array 2 (.xls)

 

Microarrays AtOligo 1.8.1.Y

Array 1 (.txt)

Array 1 (.xls)

 

Array 2 (.txt)

Array 2 (.xls)

 

Microarrays AtOligo 1.9.1.Y

Array 1 (.xls)

Array 1 (.xls)

 

Array 2 (.xls)

Array 2 (.xls)

 

Microarrays AtOligo 1.10.1.Y

Array 1 (.xls)

Array 1 (.xls)

 

Array 2 (.xls)

Array 2 (.xls)

 

Microarrays AtOligo 1.11.1.Y

Array 1 (.xls)

Array 1 (.xls)

 

Array 2 (.xls)

Array 2 (.xls)

 

Microarrays AtOligo 1.12.1.Y

Array 1 (.xls)

 

Array 2 (.xls)

 

Microarrays AtOligo 1.13.2.Y

Array (.xls)

Comments

 

Microarrays AtOligo 1.14.2.Y

Array (.txt)

 

Microarrays AtOligo 1.15.2.Y

Array (.gal)

Array (.txt)

 

Microarrays AtOligo 1.16.2.Y

Array (.gal)

Array (.xls)

 

Microarrays AtOligo 1.17.2.Y

Array (.xls)

 

Microarrays AtOligo 1.18.1.Y

Revised Feb. 16

Array 1 (.xls)

Array (.gal)

 

Array 2 (.xls)

 

Microarrays AtOligo 1.19.2.Y

Revised Jan. 23

Array (.xls)

Array (.xls)

 

Microarrays AtOligo 1.20.2.Y

Array (.xls)

 

Microarrays AtOligo 1.21.2.Y

Array (.xls)

 

Microarrays AtOligo 1.22.2.Y

Revised Dec. 2

Array (.xls)

 

Microarrays AtOligo 1.23.2.Y

Array (.xls)

 

Microarrays AtOligo 2.1.2.Y

Revised Jan. 23

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.2.2.Y

Revised Jan. 23

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.3.2.Y

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.4.2.Y

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.6.2.Y

Array (.xls)

Array (.gal)

GPL4648

Microarrays AtOligo 2.7.2.Y

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.8.2.Y

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.9.2.Y

Array (.xls)

Array (.gal)

GPL4649

Microarrays AtOligo 2.10.2.Y

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 2.11.2.Y

Revised May 14

Array (.xls)

Array (.gal)

 

Microarrays AtOligo 3.1.2.Y

Array (.xls)

Array (.gal)

GPL4650

Microarrays AtOligo 3.2.2.Y

Array (.xls)

Array (.gal)

GPL4650

*.gal = GenePix Array List file format
*Enhanced: Qiagen-Operon annotation supplemented by BLAST analyses done in the Bohnert laboratory.  For further information, please contact Hans Bohnert (bohnerth@life.uiuc.edu). 

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.  

Slide Numbering Scheme

http://ag.arizona.edu/microarray/microarrayformat.jpg



The microarrays are coded according to the following scheme:

XX refers to the lot number of the oligonucleotides. YY refers to the print run number, ZZ provides the format of the print (described above for the lookup tables).  AAA refers to the slide number within the print run.

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

 

Relating Oligo identifier to A. thaliana locus, ecotype polymorphisms, and Salk insertions:

This Excel spreadsheet (11 Mbytes) provides information linking the individual oligonucleotide elements to their corresponding gene loci.  It also provides information about the occurrence of ecotype polymorphisms, and the relationship between the loci and Salk T-DNA insertion lines.

Oligo Microarray Database:

The OMAD website (Qiagen Operon) provides a searchable database linking array oligonucleotides to gene loci.
 

Questions or comments should be addressed to: David Galbraith
Page last updated September 2, 2009