Transcript Data Availability and NASC tools

Nottingham Arabidopsis Stock Centre
http://Arabidopsis.info
NASC
Data Availability and
NASC tools
Beatrice Schildknecht
NASC
Feb 2005
Garnet.arabidopsis.org.uk
NASC Affy data
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• NASCArrays is the Affymetrix database
for Arabidopsis.
• 1567 chips (in 91 experiments) are
available for download.
• All experiments samples are fully
annotated (MIAME).
• All of the data in NASCArrays is free,
and you are free to do anything you like
with it.
The NASC Affy website
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All of our data is available via our
NASCArrays website:
http://affymetrix.arabidopsis.info
Or more simply…
affy.arabidopsis.info
• You can download all of the data in the
database for use with spreadsheets or
microarray analysis packages.
• Data is also available through some data
mining tools, such as spot history.
NASC data
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• Since 2002, NASC has operated an Affymetrix
service for customers.
• Our focus is on plant experiments, however we
have processed Affymetrix hybridisations for a
range of species.
• Included in the service are all steps after the initial
RNA extraction.
• You:
– grow your plants, extract the RNA, and send it to us.
• We:
– QC your sample before proceeding with the sample
preparation and hybridization.
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NASCarrays database
From Sample to Hybridised Array
Labelling
protocol
Extraction
protocol
Labelled RNA
RNA extract
Hybridisation
protocol
Treatment
Hybridised mix
Control
Affymetrix chip
Biological
sample
Scanning
Raw
intensity
values
Adopted from Miller et al, ‘Conforming to MIAME’
www.man.ac.uk
Hybridisation
parameters
Access data
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Browse experiments
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Keyword search
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Slide search
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Get the data
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Get the data
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The data
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NASC Tools
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• Spot History:
– Look at how your gene has performed over all experiments as a
histogram
• Gene Swinger:
– Shows experiments where your gene has been highly variable
• Two Gene Scatter Plot:
– Allows you to see how two genes performed together over all
experiments
• Bulk Gene Download:
– Allows you download a selection of genes over several
experiments
•
What is it?
•
How to use it.
Spot History
What is it?
• Data mining tool
• It shows what a
gene does over all
slides in the form
of a histogram
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Spot History
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Gene Swinger
What is it?
• Data mining tool
• Allows you to find
interesting experiments
for a gene.
• It shows you
experiments where the
gene you choose is
highly variable, over all
the experiments in the
database.
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Gene Swinger
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Gene has been
most variable!
Two gene scatterplot
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What is it?
• Data mining tool for finding interesting experiments
for genes of interest.
• It shows experiments where genes chosen are
highly variable, over all the experiments in the
database.
• Shows if genes are correlated in any way.
• It also allows you to pick slides that are different
from the general trend.
• This tool plots a scatter plot of the two genes you
select over all experiments. Every point on the
graph represents one slide.
Two gene scatterplot
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Click on an outlier
Find out which slide has behaved strangely.
Gene Bulk download
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Other sources of Data
• ArrayExpress
http://www.ebi.ac.uk/arrayexpress/
• TAIR
http://arabidopsis.org/info/expression/index.jsp
• Genevestigator
https://www.genevestigator.ethz.ch/
• AT arrays
http://atarrays.tigr.org/arabdata.shtml
• BarleyBase
http:/www.barleybase.org/
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