Zebrafish Oligo Microarray README

CD Version 2.0:  Last Modified 6/1/2005

Array Orientation and Dimensions
Naming of Design Files
Contents of Design Files
    GEML Pattern File
    GAL File
    ImaGene Files
    Tab-Delimited Files
    GEML2 File (ATTENTION: Rosetta Resolver® and Luminator® Users)
Agilent Scanner and Feature Extractor Files

Agilent Feature Extractor Error Model Parameters



This CD contains updated design files for Agilent's Zebrafish Oligo Microarray, P/N G2518A Option 001 (Agilent Microarray Design ID 013223), developed from the existing public databases. To accommodate various scanners and analysis software, the same information is provided in a variety of formats.  The CD also contains additional files that support Agilent's scanner and feature extraction software.  Any new releases or revisions to these files since production of this CD can also be found on the Agilent Microarray Design webpage and at  Agilent’s eArray  webpage.

All probe sequences are based on zebrafish (Danio rerio) public transcript and genomic sequence data.  Specific product database sources and release dates are found in the product gene list on this CD and on Agilent’s eArray webpage.

Probe sequences are not included in the files provided on this CD.  Please go to the Agilent’s eArray webpage to gain access to the microarray's 60-mer probe sequences.

Attention: This design contains e1A QC probes compatible with Agilent's RNA Spike-in Kit.

Array Orientation and Dimensions

When observing a scanned image of a slide, the image orientation can be described by specifying whether the DNA is on the front or back face of the slide, and whether the barcode is at the top, left, bottom, or right.

For example, Agilent scanners read through the glass, with the barcode to the left; the image orientation is thus DNABack_BCLeft. Axon scanners read the front of the glass with the barcode at the bottom; the image orientation is thus DNAFront_BCBottom.

The Zebrafish Oligo Microarray is a 1 array per slide format, each with 22575 features. Viewed in the Agilent standard orientation (DNABack_BCLeft), the arrays have the following dimensions:

Feature Rows:    


Feature Columns:    


Row Spacing:    

188.148 um

Column Spacing:    

211.667 um

Position of Feature 1:    

15.4 mm from left edge, 3.0 mm from top edge

In addition, the G2518A Option 001 microarray may show a stylized corner feature pattern if hybridized to a sample containing Agilent's standard positive control oligo (supplied with the Agilent Insitu Hyb Kit Plus). In the Agilent standard scan orientation, these features yield one bright spot (·) at the upper-left corner, two horizontal bright dots (··) at the upper-right corner, three bright dots in a right-angle pattern (:.) at the lower-left corner and four bright dots in a square pattern (::) at the lower-right corner.

Users of the Gene Expression Hybridization Kit may ignore this feature as the positive control oligo is not included in the kit. Agilent’s Feature Extraction v8.1 does not need stylized corner features to find the grid location of the microarray.

Naming of Design Files

The design file names comprise the following elements:

  1. Agilent Microarray Design ID - This is equal to 013223 for the G2518A Option 001 microarray. The microarray barcode includes the Agilent Microarray Design ID to enable the Agilent scanner and Feature Extraction software to automatically locate the appropriate design file.
  2. File Designator Type - Either a unique file extension (gal, txt, xml), or letter or word in the filename ( G2, MAGE, GeneID, GeneList, SequenceList).
  3. Image Orientation - For files with multiple orientations (DNAFace, BCLocation).
  4. Version date - The date on which the files were generated (YYYYMMDD). When updated versions of these design files are released to reflect changes in the annotation available for the probes, this date will be revised.

Contents of Design Files

GEML Pattern file

The GEML pattern file is an XML file conforming to the GEMLPattern document type definition (GEMLPattern.dtd). It is used by the Agilent Feature Extraction software, and the Rosetta Biosoftware Resolver and Luminator analysis software.

The GEML pattern file is named 013223_D_<YYYYMMDD>.xml.

The GEML pattern file contains one reporter element for each array feature; each reporter element in turn contains a feature element and a gene element.

The following annotation is provided:


Agilent probe identifier, in the form A_##_P<XXXXX>. This identifier uniquely identifies the probe sequence, and will never be re-used.


The accession number of a representative sequence to which the probe is designed to hybridize.  This is typically an identifier from public zebrafish sequence databases.


Description of the purpose of a probe. Control probes have a control type of "pos" or "neg". Probes to biological sequences have a control type of "false". Blank features on the array have a control type of "ignore".


The feature number in the Agilent scanner orientation (DNABack_BCLeft), counting left-to-right and top-to-bottom.


Identical to reporter systematic name.


Identical to reporter systematic name.


A functional description of the gene.


A public database in which a hit may be found.


The accession number of the hit.


The accession databases and ids collected into a single pipe-separated string.

GAL file

The GAL file is used by the Axon GenePix software. It contains the same information as the GEML file, arranged into columns. The following column mappings are used:














Accession: All accessions are combined in a pipe-separated list.

The GAL file is named 013223_D_<YYYYMMDD>.gal. Its row/column information assumes that the array has been scanned in DNAFront, BCBottom orientation.

The RefNumber column contains the feature number directly extracted from the GEML file, and can thus be used as a link between these two files.


GenePix 4.1 software does not allow specification of fractional micron feature spacing in the GAL file, even though the software supports such spacings internally.  This problem has been addressed in newer releases of the GenePix software.

BioDiscovery ImaGene GeneID Files

The GeneID files are used by the BioDiscovery Imagene software.  The GeneID file lists the probe to be found at each feature row/column, using the Agilent probe identifier. Files are provided with the feature annotation ordered in both DNABack_BarcodeLeft and DNAFront_BarcodeBottom orientation.

BioDiscovery users can generate an Imagene template file (.tpl) using the following Agilent files:



 Please consult ImaGene Help or contact BioDiscovery support for more information.

Tab-delimited files

For other users, the CD contains two tab-delimited files with the feature annotation ordered in both DNABack_BarcodeLeft and DNAFront_BarcodeBottom orientation. The column mappings in these files are equivalent to the columns in the GAL file (see above).

The tab-delimited files are named 013223_D_<DNAFace>_<BCLocation>_<YYYYMMDD>.txt

GEML2 Files (ATTENTION: Rosetta Resolver® and Luminator® Users) 

Effective March 1, 2005, Agilent is providing the GEML2 file format for Rosetta Resolver® and Luminator® users. This file allows for enhanced usability of Agilent microarray products in Resolver® and Luminator®. For future Agilent microarray products, Rosetta Resolver® and Luminator® customers should use the GEML2 file provided when loading the microarray pattern file.

Loading of the GEML2 file format for legacy Agilent microarray pattern files can be retroactively performed to your database under the guidance of Rosetta Biosoftware. Please contact Rosetta Biosoftware Support directly for more details: support@rosettabio.com.

NOTE: Only the GEML file (not GEML2) should be used with  Agilent's Feature Extraction software.The GEML2 file is named 013223_D_G2_<YYYYMMDD>.xml.

Agilent Scanner and Feature Extractor Files


Agilent logo


Instructs the XMLInstaller to autostart for PC configured to do so


Definition of the tags for the GEML pattern XML


GEML pattern file installer.


Required by the XMLInstaller


Required by the XMLInstaller


This file

To install the GEML pattern file for use by the Agilent feature extractor, insert the CD. If your PC is configured to autorun CDs then the XMLInstaller will automatically start. If it does not start automatically, then double click the XMLInstaller.exe program. The program will ask you to create a list of folders where XML files can be found, and to choose one of those folders. When a folder has been chosen, the installer will copy the GEML pattern files on the CD to the folder selected. The CD can then be removed.

If you wish to use a single installation of the design file for a network of PCs, please consult the Agilent Feature Extraction User's Manual for the required steps.

Agilent Feature Extractor Error Model Parameters

The Agilent Feature Extraction software use a parameterized error model to compute the significance (p-values) of log ratios.  The error model terms provided in the GEML pattern file are for appropriate for use with RNA target materials generated using the Agilent Linear Amplification kit.  If you are using the Agilent Direct Label kit, which generates cDNA targets, you should substitute the following error model terms on the Ratio tab of the Feature Extraction 7.5 software to enable accurate computation of the significance levels. 

Multiplicative term:    

Red Channel=0.15, Green Channel=0.25

Additive error is now calculated automatically with AutoAddErr algorithm in Feature Extraction. 

For Feature Extraction 8.1 users, please refer to Feature Extraction 8.1 default protocol and modify the multiplicative term as shown above.