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