garnet.arabidopsis.org.uk beatrice schildknecht nasc data availability and nasc tools nasc...
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Garnet.arabidopsis.org.uk
Beatrice SchildknechtNASC
Data Availability and NASC tools
NASCNottingham Arabidopsis Stock Nottingham Arabidopsis Stock CentreCentre
http://Arabidopsis.info
Feb 2005
• 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.
NASCNASC Affy dataNASC Affy data
http://affymetrix.arabidopsis.infoOr more simply…
affy.arabidopsis.info
All of our data is available via our NASCArrays website:
NASCThe NASC Affy websiteThe NASC Affy website
• 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.
• 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.
NASCNASC dataNASC data
From Sample to Hybridised Array
Biological sample
Control
RNA extract
Extraction protocol
Treatment
Affymetrix chip
Hybridisation parameters
Hybridised mix
Hybridisation protocol
Labelled RNA
Labelling protocol
Adopted from Miller et al, ‘Conforming to MIAME’ www.man.ac.uk
Scanning
Raw intensity values
NASCNASCarrays databaseNASCarrays database
NASCAccess dataAccess data
NASCBrowse experimentsBrowse experiments
NASCKeyword searchKeyword search
NASCSlide searchSlide search
NASCGet the dataGet the data
NASCGet the dataGet the data
NASCThe dataThe data
NASCNASC ToolsNASC Tools
• 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.
NASCSpot HistorySpot History
What is it?
• Data mining tool
• It shows what a gene does over all slides in the form of a histogram
NASCSpot HistorySpot History
NASCGene SwingerGene 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.
Gene has been most variable!
NASCGene SwingerGene Swinger
NASCTwo gene scatterplotTwo gene scatterplot
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.
NASCTwo gene scatterplotTwo gene scatterplot
Click on an outlier
Find out which slide has behaved strangely.
NASCGene Bulk downloadGene Bulk download
• ArrayExpresshttp://www.ebi.ac.uk/arrayexpress/
• TAIRhttp://arabidopsis.org/info/expression/index.jsp
• Genevestigatorhttps://www.genevestigator.ethz.ch/
• AT arrayshttp://atarrays.tigr.org/arabdata.shtml
• BarleyBasehttp:/www.barleybase.org/
NASCOther sources of DataOther sources of Data
NASC