Arabidopsis'info

1
Arabidopsis.info
2
Landmarks
One year ago First round opens early to allow
users to formulate applications
SEB meeting Demonstration of clustering with 24
chip data. First release of Affymetrix
Arabidopsis chip full data sets to the community
Gen Soc meeting First data set released as free
CDs to all 100 delegates
Now applications accepted at any time Still
cheaper than anywhere else at 250 Per chip all
inclusive
3
Procedures for Target Preparation
Fragment (heat, Mg2)
IVT (Biotin-UTP Biotin-CTP)
AAAA
RNA

Wash Stain
Scan
cDNA
Perfect Match
Hybridise (16 hours)
Mismatch
4
GARNet Affymetrix transcriptomics service at
NASC
Specific User
Web application
5
Processing applications
6
GARNet Affymetrix transcriptomics service at
NASC
Specific User
Web application
Request Receive RNA
Steeringcommittee
NASC service
approval
7
GARNet Affymetrix transcriptomics service at
NASC
Specific User
NASCarrays CRIME AGR
Web application
Request Receive RNA
Steeringcommittee
DATA
NASC service
approval
General Users
8
Where do I apply
9
Samples from the website
Charges
All available at affymetrix.arabidopsis.info An
d for one finger typists affy.arabidopsis.info
RNA preparation
Data analysis
Order tracking
New the NASCarrays database
The data (and AFFYwatch)
10

• Naïve user One hours work
• Data from http//arabidopsis.info/prototype/

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
Hierarchical clustering images Note the obvious
patterns of similarity (vertical stripes). Y
Genes selected by similarity. X Tissues and
ecotypes.
C
We can help you Drop-in Surgeries
11
The Customers
Round 1. 1 Ian Furner
ltijf_at_mole.bio.cam.ac.ukgt 2 Anthony Hall
ahall_at_cell.warwick.ac.uk 3 Luis Mur
lmur_at_aber.ac.uk 4 Mark Tester
mat10_at_cam.ac.uk 5 Philip White
philip-j.white_at_hri.ac.uk 6 Murray Shane
shane_at_molbiol.uct.ac.za 7 Laszlo Bogre
l.bogre_at_rhul.ac.uk 8 Jorge Casal
casal_at_ifeva.edu.ar 9 John Hammond
john.hammond_at_hri.ac.uk 10 Malcolm Campbell
malcolm.campbell_at_plants.ox.ac.uk 11 Sarah
Pritchard slp105_at_york.ac.uk 12 Hillel
Fromm h.fromm_at_leeds.ac.uk 13
Caroline Howard p.horton_at_sheffield.ac.uk 14
Paul Jarvis rpj3_at_le.ac.uk 15
Stanislaw Gawronski gawronski_at_alpha.sggw.wa
w.pl 16 Peter Doerner
peter.doerner_at_ed.ac.uk 17 Simon Geir Moller
sgm5_at_le.ac.uk 18 Patrick Gallois
patrick.gallois_at_man.ac.uk
Round 2 19. zoe wilson ltzoe.wilson_at_nottingham.ac.
ukgt 20. irene bramke lti.bramke_at_rhul.ac.ukgt 21
brian pickett ltfpicket_at_luc.edugt 22 martin mcainsh
ltm.mcainsh_at_lancaster.ac.ukgt 23 william willats
ltw.g.t.willats_at_leeds.ac.ukgt 24 maike rentel
ltmaike.rentel_at_plants.ox.ac.ukgt 25 laura Heggie
ltl.heggie_at_sheffield.ac.ukgt 26 jodi swidzinski
ltjodi.swidzinski_at_plants.ox.ac.ukgt 27 asaph
aharoni lta.aharoni_at_plant.wag-ur.nlgt 28 frank
millenaar ltf.f.millenaar_at_bio.uu.nlgt 29 raffaella
greco ltr.greco_at_plant.wag-ur.nlgt 30 alexander
grabov lta.grabov_at_ic.ac.ukgt 31 Michael Schultze
ltms47_at_york.ac.ukor 32 Hsiu ling yap
hly100_at_york.ac.uk

• Full cost hybs
• Ken Mellits
• Cathlene Eland
• Dave Twell
• Chris Harris

12
Affymetrix.arabidopsis.info
NASC GARNet John Okyere Janet Higgins David
Craigon Graeme Gill Guo-an Sun Joan Jotham Mo
Topham
Associated NASC distribution and invoicing
Louise Daugherty (NASC seed service) Emma
Humphreys (NASC seed service)
Application form design and HTML Karin Van de
Sande (GARNet)