NASC's International Affymetrix Service

Affymetrix chips can now be used for species for which they were not designed.

This has been published (see below) and all of the files and instructions are freely available (also below).

If you would like to set up a collaboration on a species not described below then please do contact us.

These files are made freely available from NASCArrays:xspecies in the understanding that they are for research purposes only, are not sold to third parties in whole or part, and that no commercial claim is made for their use beyond that described in the associated publications.. Citations for the technique and data are given below.

Xspecies files - NOTE: NEW VERSION 2.1 AVAILABLE (includes random probe removal simulation and more informative error messages)

instructions for xspecies probe generation and hybridisation.
CDF xspecies filtering perl scripts v1.1 or v2.1 - instructions for use:
1. You will need perl installed
  e.g. activeperl for windows - native for other OS
2. Download the CDF_masking.zip file or the CDF_masking_2.1.zip and unzip to your chosen location.
3. Acquire a DNA-hybridisation CEL file and an original CDF file for the same chip, put them in the CDF_masking folder***
  Examples for arabidopsis are below..
4. Run easy_script.pl (For v2.1 run the USE_ME.pl file) and follow the instructions.
Xspecies deblast and maskit scripts
deblast can be used to create CDF files from BLAST results and maskit creates CDF files from a probe list (either a CDF containing just the probes in the list or a CDF with those probes excluded).
1. To use download the CDF_writer.zip file and unzip to your chosen location.
2. Instructions for using the scripts can be downloaded here.
For Arabidopsis ATH1: ATH1-121501.CDF or for human U133+2 array - obtain from here or directly from Affymetrix.com.
**All of these scripts are (c) NASC - University of Nottingham, please ask permission before commercialisation.

References

Use of any of the files on this site or the xspecies methodology should please reference the following publications:

#1 Hammond et al (Plant Methods 2005, 1:10)
#2 Craigon et al. NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service. Nucleic Acids Research, (2004). volume 32, Database issue D575-D577.
#3 Hammond et al (New Phytologist)
#4 Cross-species Microarrays - WO2005093630

Related Publications and techniques

Same species probe improvement

#5 Graham et al. (BMC Genomics 2007, 8:344)
Neutral transcriptome xspecies analysis
#6 Broadley et al. (Evidence of neutral transcriptome evolution in plants. New Phytologist (2008) 180: 587-593)
Reviewed in 'Editors' Choice: Neutral Plantings - Science 3 October 2008; Vol. 322. no. 5898, p. 17'

Other groups independently using the xpecies approach

Cardamine Journal of Ecology 2008, 96, 1086-1097: Morinaga et al. Ecogenomics of cleistogamous and chasmogamous flowering: genome-wide gene expression patterns from cross-species microarray analysis in Cardamine kokaiensis (Brassicaceae)
Xenopus BMC Evolutionary Biology 2008, 8:43 Chain et al. Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization.

Potential issues and solutions

***I have had no probes returned / It hasn't worked Some researchers (e.g. Kate McInnerney, MSU LMPC & Functional Genomics Facility) have pointed out that most affymetrix facilities now use version 4 (binary) .CEL files. For convenience, our scripts process version 3 (text) .CEL files. You will need to convert your v4 files to v3 files with the free software available from Affymetrix in their DevNet Tools: File Manipulation section.

It takes a long time to run: The script is not optimised for old computers with small memory sizes - if it takes a long time, try a more recently purchased system.

For interest - some species already done:

On ATH1: Brassica (various), Tomato, Potato, Lettuce, Tea, Bambara, Periwinkle, Oil palm.
On Human: Axolotl, Guinea pig, Hamster, Sheep (several varieties), Horse (supported by a Horse Betting Levy Board grant), Goat, Elephant.
Banana on rice.
Goat on bovine.
Salmon/trout on zebrafish.
Grasshopper on Drosophila.

Many others have been generated with partners but may be temporarily confidential - please ask.

Further Instructions for using modified .CDF files in Genespring 7.

Delete the .arrayinfo file for the genome you are using. These files are stored in the arryinfo folder in the Genespring folder (e.g. C:\Program files\Silicon Genetics 7-2\Genespring\Data\Programs\Arrayinfo)
Select "Reanalyze samples using RMA" or "Reanalyze using GCRMA" from the external programs list
Select the samples to be reanalysed
When the "downloading array description" dialogue box appears click cancel
Select the .CDF you would like to use
The new samples will then be created and can be used to create new experiments using sample manager