Data Availability and NASC tools - University of Nottingham

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 NASC 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 NASC 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 NASC 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. NASCarrays database NASC

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 NASC Browse experiments NASC Keyword search

NASC Slide search NASC Get the data NASC

Get the data NASC The data NASC NASC Tools NASC

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 NASC Spot History NASC

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. NASC Gene Swinger NASC Gene has been most variable!

Two gene scatterplot NASC 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 NASC

Click on an outlier Find out which slide has behaved strangely. Gene Bulk download NASC 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/ NASC NASC

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