Affymetrix Service

1
Affymetrix Service Nottingham Arabidopsis Stock
Centre - Garnet Resources http//arabidopsis.info
/prototype
Sarah Cannell, David J Craigon, Louise
Daugherty, Penny Dennis, Graeme Gill, Janet
Higgins, Emma Humphreys, Joan Jotham, John
Okyere, Guo-an Sun, Mo Topham, Lin Zhang, Sean T
May Nottingham Arabidopsis Stock Centre, Plant
Science Division, University of Nottingham,
Sutton Bonington Campus, Loughborough LE12 5RD,
UK

• The Service
• NASC provides a full hybridisation and data
  warehousing Affymetrix Genechip Service

NASC provides an Affymetrix Genechip service for
the UK Arabidopsis post-genomics consortium
(GARNet). The equipment for this service (shown
in the panel to the right) was funded by the
BBSRC and installed at NASC in January 2002.

• The GeneChip
• Currently 8200 genes.
• Full genome coverage from May 2002 (
  25,000 genes)

The chip that we have been using was developed by
Affymetrix and Novartis from a set of 8200
predicted genes derived from BAC sequence,
complemented by more than 100 EST clusters. Each
gene is represented by multiple short
oligonucleotides that have been synthesised
in-situ into a high density array.
The service is entirely web based and proceeds
according to the following plan
Specific User
NASCarrays CRIME AGR

• Apply for our service through GARNet
• http//garnet.arabidopsis.org.uk

Web application
Request Receive RNA

• Data Release
• All data will be made public.

Steeringcommittee
DATA
NASC service
General Users
approval
Once RNA arrives at NASC, we perform Agilent
Bioanaliser 2100 quality control analysis to
confirm RNA integrity.

• Free Affymetrix data available now
• http//arabidopsis.info/prototype/

The QC electropherograms are returned to the user
and made available for future users. Given RNA of
suitable quality we generate cRNA confirm
labelling by RNA chip pre-test the materials
with the test3 test chip and then perform the
actual final hybridisation.
A
B
Our first set of data using the 8200 Novartis
Affymetrix chip allows a simple clustering
comparison using EPCLUST from the EBI. The
complementary images here cluster genes that are
co-expressed in 3 ecotypes (Col, Ler Ws) A.
Cotyledons up Other tissues off. B.
All tissues up Cotyledons. off. C.
Ecotype 1 3 all tissues off Ecotype 2,
Cotyledons off Ecotype 2, Other
tissues. up
All of the data that we generate are made freely
and publicly available through the web. Our first
baseline experiments were intended to set up a
precedent for good practice in deriving
Arabidopsis staged tissues from defined ecotypes.
This has allowed us to perform some basic
clustering analyses that can be replicated and/or
mined by the general community.
Hierarchical clustering images Note the obvious
patterns of similarity (vertical stripes). Y
Genes selected by similarity. X Tissues and
ecotypes.
NASC
C