Affymetrix chips can now be used for species for which they were not designed.
This is published (see below) and all of the files to reproduce it are freely available.
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 and that no 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 2.0 AVAILABLE (includes random probe removal simulation)
- instructions for xspecies probe generation and hybridisation.
- CDF xspecies filtering perl scripts v1.1 or v2.0 - instructions for use:
- You will need perl installed
e.g. activeperl for windows - native for other OS - Download the CDF_masking.zip file or the CDF_masking_2.0.zip and unzip to your chosen location.
- 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.. - Run easy_script.pl (For v2.0 run the USE_ME.pl file) and follow the instructions.
For Arabidopsis ATH1: ATH1-121501.CDF - obtain from here or directly from Affymetrix.com.
- You will need perl installed
Example CDFs:
- Brassica on ATH1
- Tomato on ATH1
- Potato on ATH1
- Lettuce on ATH1
- Tea on ATH1
- Bambara on ATH1
- Banana on rice
- Axolotl on human
- Guinea pig on human
- Hamster on human
- Sheep on human
- Horse on human
- Goat on human and bovine
- Salmon/trout on zebrafish
- Grasshopper on Drosophila
'Same species' DNA .CEL filesfrom Graham et al #5ArabidopsisRice
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Please note that many of these files are Large and will take a long time to load
If you wish to be sent the files on CD please contact NASCarrays at
this address
Use of any of these files 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
- #5 Graham et al. (BMC Genomics 2007, 8:344)
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 noted that most affymetrix facilities use version 4 (binary) .CEL files. Our scripts process version 3 (text) .CEL files. You will need to convert these with the free software available from Affymetrix in their DevNet Tools: File Manipulation section.It takes forever to run: The script is not optimised for computers with small memory sizes - if it takes a long time, try a more recently purchased system.
Using modified .CDF files in Genespring
- 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
Brassica oleracea filesfrom Hammond et al #1
DNA .CEL file (zipped)RNA .CEL files (zipped)
Script generated (masked) CDF files
Thlaspi arvense filesfrom Hammond et al #3
DNA .CEL file (zipped)RNA .CEL files (zipped)
Thlaspi caerulescens filesfrom Hammond et al #3
DNA .CEL file (zipped)RNA .CEL files (zipped) |