 |
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 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) | |||
| 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) | |||
| 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) | |||
| Microarrays AtOligo 3.2.2.Y | Array (.xls) | Array (.gal) |
*.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
|
|
 |
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.
Page last updated December 14, 2006