NASCArrays:Xspecies

Cross species methods for Affymetrix chips.

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

Simple guide

  • Step 1: Label and hybridise species X genomic DNA to an affy chip [lab instructions ]
  • Step 2: Make a new CDF for your species
  • Step 3: Use your new CDF to analyse RNA hybs for your new species.

Quikstart (zip) packages including scripts, instructions and CDFs

Quikstart for U133plus2.0 human chips
Quikstart for HG-U133+ PM plates
Quikstart for ATH1 arabidopsis chips

The unzipped folders are ready to drop in a v3 DNA hyb .cel and churn out a range of xspecies CDFs and a graph of results.

Recommended for people who have read one of the papers (right).

These folders can be used for other chips simply by substituting the CDF.

Detailed Xspecies files (for automation see quikstart above)

  1. You will need perl installed
    e.g. activeperl for windows
  2. You will need a v3 DNA-hybridisation CEL file (see 'examples') and an original CDF file for the same chip:
  3. Download the archive, unzip, drop in the CEL and CDF files, and run USE_ME.pl (e.g. perl USE_ME.pl on the command line).

Specialist Xspecies deblast and maskit scripts

  1. deblast creates CDF files from BLAST results
  2. 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).
  3. [zip archive] | [Instructions]

Troubleshooting

It doesn't work
Most affy users now have v4/v5 binary .CEL files
Our scripts need v3 (text) .CEL files.
Free conversion software:

It takes a long time to run: Try a more modern computer - The script is a memory hog.

Using modified .CDF files in Bioconductor (affylmGUI).

with thanks to Hugh Shanahan

Instructions for xspecies e.g. zombie_100.cdf on human.

  • install makecdfenv
  • library(makecdfenv)
    make.cdf.package("zombie_100.cdf", packagename="zombiecdf", species="homo_sapiens")
  • install.packages("zombiecdf", repos=NULL, type="source")
  • in affylmgui (after loading targets), Evaluate:
    RawAffyData@cdfName <- "zombiecdf"

  • More detailed instructions

Using modified .CDF files in Genespring 9 / 10.

  • Using the modified .CDF file: Tools > Create Custom Technology > Affymetrix Expression). Annotation
  • Change the array name in the header of the RNA .CEL files (must be converted to version 3 and edited in Notepad or Wordpad). The new name must be identical to the custom technology that you have just made e.g. change ATH1-12501.1sq or HG-U133_Plus_2.1sq to xspecies_1.1sq
  • Create a new experiment using the modified .CEL files

Using modified .CDF files in Genespring 11.5.

  • Annotations>create technology>Affymetrix Expression
  • mammoth_100.cdf produces Affymetrix.GeneChip.mammoth_100
  • Edit your v3 .cels on the DatHeader= line (replace xxx.1sq with mammoth_100.1sq)
  • Create new project> create new experiment> [Affymetrix expression]
    Select technology > Affymetrix.GeneChip.hamster_100
    Choose the edited cel v3's
    You will get a message that [ probes matched = xxxxx ]
    Which should be the same as detailed in your CDF: NumberOfUnits=xxxxx

contact us.

Some species already done:

Brassicaceae (various), Tomato, Potato, Lettuce, Tea, Bambara, Periwinkle, Oil palm. Guinea pig, Hamster, Sheep (several varieties), Horse, Elephant, Brassicaceae (various), Tomato, Aloe, Rubber, Lettuce, Tea, Bambara, Periwinkle, Oil palm, Banana, Grasshopper, Bees. Many others - please ask.

Publications

Example Data

Brassica oleracea files

Paper

Thlaspi arvense and caerulescens

paper

'Same species' DNA .CEL files

Neutral Evolution (crucifer example)

Musa (banana) files

Horse files

Sheep files